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13 pages, 2539 KiB

Open AccessArticle

Microsatellite Dataset for Cultivar Discrimination in Spring Orchid (Cymbidium goeringii)

by Da Eun Nam, Min Ju Cha, Yae Dam Kim, Manisha Awasthi, Yuno Do, Sam-Geun Kong and Ki Wha Chung

Genes 2023, 14(8), 1610; https://doi.org/10.3390/genes14081610 - 11 Aug 2023

Viewed by 895

Abstract

Cymbidium goeringii Reichb. fil., locally known as the spring orchid in the Republic of Korea, is one of the most important and popular horticultural species in the family Orchidaceae. C. goeringii cultivars originated from plants with rare phenotypes in wild mountains where pine [...] Read more.

Cymbidium goeringii Reichb. fil., locally known as the spring orchid in the Republic of Korea, is one of the most important and popular horticultural species in the family Orchidaceae. C. goeringii cultivars originated from plants with rare phenotypes in wild mountains where pine trees commonly grow. This study aimed to determine the cultivar-specific combined genotypes (CGs) of short sequence repeats (SSRs) by analyzing multiple samples per cultivar of C. goeringii. In this study, we collected more than 4000 samples from 67 cultivars and determined the genotypes of 12 SSRs. Based on the most frequent combined genotypes (CG1s), the average observed allele number and combined matching probability were 11.8 per marker and 3.118 × 10⁻¹¹, respectively. Frequencies of the CG1 in 50 cultivars (n ≥ 10) ranged from 40.9% to 100.0%, with an average of 70.1%. Assuming that individuals with the CG1 are genuine in the corresponding cultivars, approximately 30% of C. goeringii on the farms and markets may be not genuine. The dendrogram of the phylogenetic tree and principal coordinate analysis largely divided the cultivars into three groups according to their countries of origin; however, the genetic distances were not great among the cultivars. In conclusion, this dataset of C. goeringii cultivar-specific SSR profiles could be used for ecogenetic studies and forensic authentication. This study suggests that genetic authentication should be introduced for the sale of expensive C. goeringii cultivars. We believe that this study will help establish a genetic method for the forensic authentication of C. goeringii cultivars. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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10 pages, 4200 KiB

Open AccessArticle

US Population Data for 94 Identity-Informative SNP Loci

by Kevin M. Kiesler, Lisa A. Borsuk, Carolyn R. Steffen, Peter M. Vallone and Katherine B. Gettings

Genes 2023, 14(5), 1071; https://doi.org/10.3390/genes14051071 - 12 May 2023

Cited by 1 | Viewed by 1494

Abstract

The US National Institute of Standards and Technology (NIST) analyzed a set of 1036 samples representing four major US population groups (African American, Asian American, Caucasian, and Hispanic) with 94 single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs). The compact size of [...] Read more.

The US National Institute of Standards and Technology (NIST) analyzed a set of 1036 samples representing four major US population groups (African American, Asian American, Caucasian, and Hispanic) with 94 single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs). The compact size of iiSNP amplicons compared to short tandem repeat (STR) markers increases the likelihood of successful amplification with degraded DNA samples. Allele frequencies and relevant forensic statistics were calculated for each population group as well as the aggregate population sample. Examination of sequence data in the regions flanking the targeted SNPs identified additional variants, which can be combined with the target SNPs to form microhaplotypes (multiple phased SNPs within a short-read sequence). Comparison of iiSNP performance with and without flanking SNP variation identified four amplicons containing microhaplotypes with observed heterozygosity increases of greater than 15% over the targeted SNP alone. For this set of 1036 samples, comparison of average match probabilities from iiSNPs with the 20 CODIS core STR markers yielded an estimate of 1.7 × 10⁻³⁸ for iiSNPs (assuming independence between all 94 SNPs), which was four orders of magnitude lower (more discriminating) than STRs where internal sequence variation was considered, and 10 orders of magnitude lower than STRs using established capillary electrophoresis length-based genotypes. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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18 pages, 10922 KiB

Open AccessArticle

Evaluation of Library Preparation Workflows and Applications to Different Sample Types Using the PowerSeq^® 46GY System with Massively Parallel Sequencing

by Kyleen Elwick, Patrick Rydzak and James M. Robertson

Genes 2023, 14(5), 977; https://doi.org/10.3390/genes14050977 - 26 Apr 2023

Cited by 2 | Viewed by 1354

Abstract

This project evaluated the prototype PowerSeq^® 46GY System using donor DNA and casework-type samples. The goal of this study was to determine whether modifications to the manufacturer’s protocol could increase read coverage and improve sample results. Buccal and casework-type libraries were prepared [...] Read more.

This project evaluated the prototype PowerSeq^® 46GY System using donor DNA and casework-type samples. The goal of this study was to determine whether modifications to the manufacturer’s protocol could increase read coverage and improve sample results. Buccal and casework-type libraries were prepared using the TruSeq^® DNA PCR-Free HT kit or the KAPA HyperPrep kit. Both kits were evaluated unmodified, and by substituting AMPure^® XP beads for the beads of the most optimal kit. Two qPCR kits, the PowerSeq^® Quant MS System and KAPA Library Quantification Kit, were also evaluated along with a KAPA size-adjustment workbook, which was compared as a third quantification method. Libraries were sequenced using the MiSeq^® FGx and data were analyzed with STRait Razor. Results suggested that all three quantification methods overestimated library concentration, but the PowerSeq kit was most accurate. Samples prepared with the TruSeq library kit provided the highest coverage and the fewest instances of dropout and below-threshold alleles compared with the KAPA kit. Additionally, all bone and hair samples demonstrated full profile completeness, with bone samples yielding a higher average coverage than hair samples. Overall, our study demonstrated that the 46GY manufacturer’s protocol produced the best quality results compared to alternative library preparation options. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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12 pages, 1262 KiB

Open AccessArticle

Association between Variants in the OCA2-HERC2 Region and Blue Eye Colour in HERC2 rs12913832 AA and AG Individuals

by Nina Mjølsnes Salvo, Jeppe Dyrberg Andersen, Kirstin Janssen, Olivia Luxford Meyer, Thomas Berg, Claus Børsting and Gunn-Hege Olsen

Genes 2023, 14(3), 698; https://doi.org/10.3390/genes14030698 - 11 Mar 2023

Cited by 2 | Viewed by 2538

Abstract

The OCA2-HERC2 region is strongly associated with human pigmentation, especially eye colour. The HERC2 SNP rs12913832 is currently the best-known predictor for blue and brown eye colour. However, in a previous study we found that 43 of 166 Norwegians with the brown eye [...] Read more.

The OCA2-HERC2 region is strongly associated with human pigmentation, especially eye colour. The HERC2 SNP rs12913832 is currently the best-known predictor for blue and brown eye colour. However, in a previous study we found that 43 of 166 Norwegians with the brown eye colour genotype rs12913832:AA or AG, did not have the expected brown eye colour. In this study, we carried out massively parallel sequencing of a ~500 kbp HERC2-OCA2 region in 94 rs12913832:AA and AG Norwegians (43 blue-eyed and 51 brown-eyed) to search for novel blue eye colour variants. The new candidate variants were subsequently typed in a Norwegian biobank population (total n = 519) for population specific association analysis. We identified five new variants, rs74409036:A, rs78544415:T, rs72714116:T, rs191109490:C and rs551217952:C, to be the most promising candidates for explaining blue eye colour in individuals with the rs12913832:AA and AG genotype. Additionally, we confirmed the association of the missense variants rs74653330:T and rs121918166:T with blue eye colour, and observed lighter skin colour in rs74653330:T individuals. In total, 37 (86%) of the 43 blue-eyed rs12913832:AA and AG Norwegians could potentially be explained by these seven variants, and we suggest including them in future prediction models. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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10 pages, 739 KiB

Open AccessArticle

NIPAT as Non-Invasive Prenatal Paternity Testing Using a Panel of 861 SNVs

by Riccardo Giannico, Luca Forlani, Valentina Andrioletti, Ettore Cotroneo, Andrea Termine, Carlo Fabrizio, Raffaella Cascella, Luca Salvaderi, Pasquale Linarello, Debora Varrone, Laura Gigante and Emiliano Giardina

Genes 2023, 14(2), 312; https://doi.org/10.3390/genes14020312 - 25 Jan 2023

Viewed by 2398

Abstract

In 1997, it was discovered that maternal plasma contains Cell-Free Fetal DNA (cffDNA). cffDNA has been investigated as a source of DNA for non-invasive prenatal testing for fetal pathologies, as well as for non-invasive paternity testing. While the advent of Next Generation Sequencing [...] Read more.

In 1997, it was discovered that maternal plasma contains Cell-Free Fetal DNA (cffDNA). cffDNA has been investigated as a source of DNA for non-invasive prenatal testing for fetal pathologies, as well as for non-invasive paternity testing. While the advent of Next Generation Sequencing (NGS) led to the routine use of Non-Invasive Prenatal Screening (NIPT or NIPS), few data are available regarding the reliability and reproducibility of Non-Invasive Prenatal Paternity Testing (NIPPT or NIPAT). Here, we present a non-invasive prenatal paternity test (NIPAT) analyzing 861 Single Nucleotide Variants (SNV) from cffDNA through NGS technology. The test, validated on more than 900 meiosis samples, generated log(CPI)(Combined Paternity Index) values for designated fathers ranging from +34 to +85, whereas log(CPI) values calculated for unrelated individuals were below −150. This study suggests that NIPAT can be used with high accuracy in real cases. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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16 pages, 1926 KiB

Open AccessArticle

Development and Validation of MPS-Based System for Human Appearance Prediction in Challenging Forensic Samples

by Filomena Melchionda, Beatrice Silvestrini, Carlo Robino, Carla Bini, Paolo Fattorini, Cristina Martinez-Labarga, Flavio De Angelis, Adriano Tagliabracci and Chiara Turchi

Genes 2022, 13(10), 1688; https://doi.org/10.3390/genes13101688 - 21 Sep 2022

Cited by 3 | Viewed by 2236

Abstract

Forensic DNA phenotyping (FDP) provides the ability to predict the human external traits from unknown sample donors, directly from minute amounts of DNA found at the crime scene. We developed a MPS multiplex assay, with the aim of genotyping all 41 DNA markers [...] Read more.

Forensic DNA phenotyping (FDP) provides the ability to predict the human external traits from unknown sample donors, directly from minute amounts of DNA found at the crime scene. We developed a MPS multiplex assay, with the aim of genotyping all 41 DNA markers included in the HIrisPlex-S system for simultaneous prediction of eye, hair and skin colours. Forensic samples such as blood, skeletal remains, touch DNA, saliva swab, artificially degraded samples together with individuals with known phenotypes and a set of 2800 M control DNA were sequenced on the Ion Torrent platform in order to evaluate the concordance testing results and the forensic suitability of the 41-plex MPS assay. The panel was evaluated by testing a different number of PCR cycles and the volume of reagents for library preparation. The study demonstrated that full and reliable profiles were obtained with 0.1–5 ng, even with high degraded DNA. The increment of the number of PCR cycles results in an improvement of correctly genotyping and phenotyping for samples with low amounts of degraded DNA but higher frequencies of artefacts were found. The high DNA degradation level did not influence the correct genotyping and phenotyping and the critical parameter affecting the result is the quantity of input DNA. Eye and hair colour was predicted in 92.60% of individuals and skin colour in 85.15% of individuals. The results suggest that this MPS assay is robust, highly sensitive and useful for human pigmentation prediction in the forensic genetic field. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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15 pages, 438 KiB

Open AccessArticle

Integrity, Trustworthiness, and Effectiveness: Towards an Ethos for Forensic Genetics

by Matthias Wienroth, Aaron Opoku Amankwaa and Carole McCartney

Genes 2022, 13(8), 1453; https://doi.org/10.3390/genes13081453 - 16 Aug 2022

Cited by 4 | Viewed by 2698

Abstract

Forensic genetics comes under critical scrutiny when developments challenge previously accepted legal, ethical, social, and other boundaries. Forensic geneticists continue to build a knowledge culture within a community of practice that acknowledges ethical standards of conduct in both research and the societal application [...] Read more.

Forensic genetics comes under critical scrutiny when developments challenge previously accepted legal, ethical, social, and other boundaries. Forensic geneticists continue to build a knowledge culture within a community of practice that acknowledges ethical standards of conduct in both research and the societal application of forensic genetics. As the community further cements and extends its societal role, and in that process often pushing at ethical and legal boundaries, it requires a strong, resilient, and responsive ethos that, in setting clear parameters for conduct, fosters the field’s sense of purpose. While supra-national declarations and human rights protections, coupled with local regulations, provide some parameters for practice, and discipline-specific guidance has refined an agenda for forensic genetics research and application, this maturing field needs to now define its core principles. This contribution proposes the values of integrity, trustworthiness, and effectiveness as a foundational triptych for a bespoke forensic genetics ethos to ensure the augmentation of developments that range from a purely science-oriented to a wider societally relevant knowledge culture. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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15 pages, 2217 KiB

Open AccessArticle

Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach

by Irena Zupanič Pajnič, Tomaž Zupanc, Tamara Leskovar, Matija Črešnar and Paolo Fattorini

Genes 2022, 13(8), 1432; https://doi.org/10.3390/genes13081432 - 12 Aug 2022

Cited by 7 | Viewed by 1968

Abstract

To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd [...] Read more.

To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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38 pages, 5163 KiB

Open AccessArticle

Internal Validation of MaSTR™ Probabilistic Genotyping Software for the Interpretation of 2–5 Person Mixed DNA Profiles

by Michael S. Adamowicz, Taylor N. Rambo and Jennifer L. Clarke

Genes 2022, 13(8), 1429; https://doi.org/10.3390/genes13081429 - 11 Aug 2022

Cited by 3 | Viewed by 1915

Abstract

Mixed human deoxyribonucleic acid (DNA) samples present one of the most challenging pieces of evidence that a forensic analyst can encounter. When multiple contributors, stochastic amplification, and allele drop-out further complicate the mixture profile, interpretation by hand becomes unreliable and statistical analysis problematic. [...] Read more.

Mixed human deoxyribonucleic acid (DNA) samples present one of the most challenging pieces of evidence that a forensic analyst can encounter. When multiple contributors, stochastic amplification, and allele drop-out further complicate the mixture profile, interpretation by hand becomes unreliable and statistical analysis problematic. Probabilistic genotyping software has provided a tool to address complex mixture interpretation and provide likelihood ratios for defined sets of propositions. The MaSTR™ software is a fully continuous probabilistic system that considers a wide range of STR profile data to provide likelihood ratios on DNA mixtures. Mixtures with two to five contributors and a range of component ratios and allele peak heights were created to test the validity of MaSTR™ with data similar to real casework. Over 280 different mixed DNA profiles were used to perform more than 2600 analyses using different sets of propositions and numbers of contributors. The results of the analyses demonstrated that MaSTR™ provided accurate and precise statistical data on DNA mixtures with up to five contributors, including minor contributors with stochastic amplification effects. Tests for both Type I and Type II errors were performed. The findings in this study support that MaSTR™ is a robust tool that meets the current standards for probabilistic genotyping. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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10 pages, 2834 KiB

Open AccessArticle

State of the Art for Microhaplotypes

by Kenneth K. Kidd and Andrew J. Pakstis

Genes 2022, 13(8), 1322; https://doi.org/10.3390/genes13081322 - 24 Jul 2022

Cited by 15 | Viewed by 2535

Abstract

In recent years, the number of publications on microhaplotypes has averaged more than a dozen papers annually. Many have contributed to a significant increase in the number of highly polymorphic microhaplotype loci. This increase allows microhaplotypes to be very informative in four main [...] Read more.

In recent years, the number of publications on microhaplotypes has averaged more than a dozen papers annually. Many have contributed to a significant increase in the number of highly polymorphic microhaplotype loci. This increase allows microhaplotypes to be very informative in four main areas of forensic uses of DNA: individualization, ancestry inference, kinship analysis, and mixture deconvolution. The random match Probability (RMP) can be as small as 10⁻¹⁰⁰ for a large panel of microhaplotypes. It is possible to measure the heterozygosity of an MH as the effective number of alleles (A_e). A_e > 7.5 exists for African populations and >4.5 exists for Native American populations for a smaller panel of two dozen selected microhaplotypes. Using STRUCTURE, at least 10 different ancestral clusters can be defined by microhaplotypes. The A_e for a locus is also identical to the Paternity Index (PI), the measure of how informative a locus will be in parentage testing. High A_e loci can also be useful in missing persons cases. Finally, high A_e microhaplotypes allow the near certainty of seeing multiple additional alleles in a mixture of two or more individuals in a DNA sample. In summary, a panel of higher A_e microhaplotypes can outperform the standard CODIS markers. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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10 pages, 1541 KiB

Open AccessArticle

Cell Subsampling Recovers Probative DNA Profile Information from Unresolvable/Undetectable Minor Donors in Mixtures

by Kaitlin Huffman, Erin Hanson and Jack Ballantyne

Genes 2022, 13(7), 1117; https://doi.org/10.3390/genes13071117 - 22 Jun 2022

Cited by 8 | Viewed by 1749

Abstract

When a minor DNA component to a binary mixture is present at a weight ratio of approximately 1:50 or less, the presence of this minor donor is undetectable (or barely detectable) by standard mixture deconvolution approaches. In an attempt to retrieve probative minor [...] Read more.

When a minor DNA component to a binary mixture is present at a weight ratio of approximately 1:50 or less, the presence of this minor donor is undetectable (or barely detectable) by standard mixture deconvolution approaches. In an attempt to retrieve probative minor donor DNA profile information, multiple quintuple cell subsamples were collected from a 1:50 DNA mixture using direct single cell subsampling (DSCS) paired with probabilistic genotyping (PG), the latter validated for use with single or few cells. DSCS employs a simplified micromanipulation technique paired with an enhanced DNA profiling approach, involving direct cell lysis and a sensitive PCR process, to genotype individual cells. Multiple five-cell subsamples were used to interrogate sufficient cells from the mixture such that some of the created 5-cell “mini-mixture” subsamples contained a cell from the minor donor. The latter mini-mixture subsamples, which now comprised weight ratios of 1:4 as opposed to the bulk mixture 1:50, were analyzed with the PG systems STRmix^TM and EuroForMix resulting in a significant probative gain of information, (LR ≅ 10¹¹, compared to standard bulk mixture PG methods, LR ≅ 10¹–10²). Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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17 pages, 1339 KiB

Open AccessArticle

Evaluation of the Effects of Different Sample Collection Strategies on DNA/RNA Co-Analysis of Forensic Stains

by Daniela Lacerenza, Giorgio Caudullo, Elena Chierto, Serena Aneli, Giancarlo Di Vella, Marco Barberis, Samuele Voyron, Paola Berchialla and Carlo Robino

Genes 2022, 13(6), 983; https://doi.org/10.3390/genes13060983 - 30 May 2022

Cited by 2 | Viewed by 2268

Abstract

The aim of this study was to evaluate the impact of different moistening agents (RNase-free water, absolute anhydrous ethanol, RNAlater^®) applied to collection swabs on DNA/RNA retrieval and integrity for capillary electrophoresis applications (STR typing, cell type identification by mRNA profiling). [...] Read more.

The aim of this study was to evaluate the impact of different moistening agents (RNase-free water, absolute anhydrous ethanol, RNAlater^®) applied to collection swabs on DNA/RNA retrieval and integrity for capillary electrophoresis applications (STR typing, cell type identification by mRNA profiling). Analyses were conducted on whole blood, luminol-treated diluted blood, saliva, semen, and mock skin stains. The effects of swab storage temperature and the time interval between sample collection and DNA/RNA extraction were also investigated. Water provided significantly higher DNA yields than ethanol in whole blood and semen samples, while ethanol and RNAlater^® significantly outperformed water in skin samples, with full STR profiles obtained from over 98% of the skin samples collected with either ethanol or RNAlater^®, compared to 71% of those collected with water. A significant difference in mRNA profiling success rates was observed in whole blood samples between swabs treated with either ethanol or RNAlater^® (100%) and water (37.5%). Longer swab storage times before processing significantly affected mRNA profiling in saliva stains, with the success rate decreasing from 91.7% after 1 day of storage to 25% after 7 days. These results may contribute to the future development of optimal procedures for the collection of different types of biological traces. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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16 pages, 1843 KiB

Open AccessArticle

Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA

by Marianne Dehasque, Patrícia Pečnerová, Vendela Kempe Lagerholm, Erik Ersmark, Gleb K. Danilov, Peter Mortensen, Sergey Vartanyan and Love Dalén

Genes 2022, 13(4), 687; https://doi.org/10.3390/genes13040687 - 13 Apr 2022

Cited by 6 | Viewed by 3890

Abstract

Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, [...] Read more.

Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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Review

Jump to: Research

30 pages, 2632 KiB

Open AccessReview

Indirect DNA Transfer and Forensic Implications: A Literature Review

by Francesco Sessa, Cristoforo Pomara, Massimiliano Esposito, Patrizia Grassi, Giuseppe Cocimano and Monica Salerno

Genes 2023, 14(12), 2153; https://doi.org/10.3390/genes14122153 - 28 Nov 2023

Cited by 3 | Viewed by 2451

Abstract

Progress in DNA profiling techniques has made it possible to detect even the minimum amount of DNA at a crime scene (i.e., a complete DNA profile can be produced using as little as 100 pg of DNA, equivalent to only 15–20 human cells), [...] Read more.

Progress in DNA profiling techniques has made it possible to detect even the minimum amount of DNA at a crime scene (i.e., a complete DNA profile can be produced using as little as 100 pg of DNA, equivalent to only 15–20 human cells), leading to new defense strategies. While the evidence of a DNA trace is seldom challenged in court by a defendant’s legal team, concerns are often raised about how the DNA was transferred to the location of the crime. This review aims to provide an up-to-date overview of the experimental work carried out focusing on indirect DNA transfer, analyzing each selected paper, the experimental method, the sampling technique, the extraction protocol, and the main results. Scopus and Web of Science databases were used as the search engines, including 49 papers. Based on the results of this review, one of the factors that influence secondary transfer is the amount of DNA shed by different individuals. Another factor is the type and duration of contact between individuals or objects (generally, more intimate or prolonged contact results in more DNA transfer). A third factor is the nature and quality of the DNA source. However, there are exceptions and variations depending on individual characteristics and environmental conditions. Considering that secondary transfer depends on multiple factors that interact with each other in unpredictable ways, it should be considered a complex and dynamic phenomenon that can affect forensic investigation in various ways, for example, placing a subject at a crime scene who has never been there. Correct methods and protocols are required to detect and prevent secondary transfer from compromising forensic evidence, as well as the correct interpretation through Bayesian networks. In this context, the definition of well-designed experimental studies combined with the use of new forensic techniques could improve our knowledge in this challenging field, reinforcing the value of DNA evidence in criminal trials. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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12 pages, 275 KiB

Open AccessReview

The Role of miRNA Expression Profile in Sudden Cardiac Death Cases

by Alessia Bernini Di Michele, Valerio Onofri, Mauro Pesaresi and Chiara Turchi

Genes 2023, 14(10), 1954; https://doi.org/10.3390/genes14101954 - 17 Oct 2023

Viewed by 1290

Abstract

Sudden cardiac death (SCD) is one of the leading causes of death in the world and for this reason it has attracted the attention of numerous researchers in the field of legal medicine. It is not easy to determine the cause in a [...] Read more.

Sudden cardiac death (SCD) is one of the leading causes of death in the world and for this reason it has attracted the attention of numerous researchers in the field of legal medicine. It is not easy to determine the cause in a SCD case and the available methods used for diagnosis cannot always give an exhaustive answer. In addition, the molecular analysis of genes does not lead to a clear conclusion, but it could be interesting to focus attention on the expression level of miRNAs, a class of non-coding RNA of about 22 nucleotides. The role of miRNAs is to regulate the gene expression through complementary binding to 3′-untraslated regions of miRNAs, leading to the inhibition of translation or to mRNA degradation. In recent years, several studies were performed with the aim of exploring the use of these molecules as biomarkers for SCD cases, and to also distinguish the causes that lead to cardiac death. In this review, we summarize experiments, evidence, and results of different studies on the implication of miRNAs in SCD cases. We discuss the different biological starting materials with their respective advantages and disadvantages, studying miRNA expression on tissue (fresh-frozen tissue and FFPE tissue), circulating cell-free miRNAs in blood of patients affected by cardiac disease at high risk of SCD, and exosomal miRNAs analyzed from serum of people who died from SCD. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

16 pages, 2904 KiB

Open AccessEditor’s ChoiceReview

Bridging Disciplines to Form a New One: The Emergence of Forensic Genetic Genealogy

by Claire L. Glynn

Genes 2022, 13(8), 1381; https://doi.org/10.3390/genes13081381 - 01 Aug 2022

Cited by 15 | Viewed by 9388

Abstract

Forensic Genetic Genealogy (FGG) has fast become a popular tool in criminal investigations since it first emerged in 2018. FGG is a novel investigatory tool that has been applied to hundreds of unresolved cold cases in the United States to generate investigative leads [...] Read more.

Forensic Genetic Genealogy (FGG) has fast become a popular tool in criminal investigations since it first emerged in 2018. FGG is a novel investigatory tool that has been applied to hundreds of unresolved cold cases in the United States to generate investigative leads and identify unknown individuals. Consumer DNA testing and the public’s increased curiosity about their own DNA and genetic ancestry, have greatly contributed to the availability of human genetic data. Genetic genealogy has been a field of study/interest for many years as both amateur and professional genetic genealogists use consumer DNA data to explore genetic connections in family trees. FGG encompasses this knowledge by applying advanced sequencing technologies to forensic DNA evidence samples and by performing genetic genealogy methods and genealogical research, to produce possible identities of unknown perpetrators of violent crimes and unidentified human remains. This combination of forensic genetics, genetic genealogy, and genealogical research has formed a new subdiscipline within the forensic sciences. This paper will summarize the individual disciplines that led to the emergence of FGG, its practice in forensic investigations, and current/future considerations for its use. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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14 pages, 1860 KiB

Open AccessReview

On the Forensic Use of Y-Chromosome Polymorphisms

by Peter de Knijff

Genes 2022, 13(5), 898; https://doi.org/10.3390/genes13050898 - 17 May 2022

Cited by 7 | Viewed by 5126

Abstract

Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, [...] Read more.

Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, I will sketch a brief history focusing on the forensic use of Y-chromosome polymorphisms. Before describing the various applications of short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) on the Y-chromosome, I will discuss a few often ignored aspects influencing proper use and interpretation of Y-chromosome information: (i) genotyping Y-SNPs and Y-STRs, (ii) Y-STR haplotypes shared identical by state (IBS) or identical by descent (IBD), and (iii) Y-haplotype database frequencies. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)

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