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Gerontology 2018Forensic genetics developed from protein-based techniques a quarter of a century ago and became famous as "DNA fingerprinting," this being based on restriction fragment... (Review)
Review
Forensic genetics developed from protein-based techniques a quarter of a century ago and became famous as "DNA fingerprinting," this being based on restriction fragment length polymorphisms (RFLPs) of high-molecular-weight DNA. The amplification of much smaller short tandem repeat (STR) sequences using the polymerase chain reaction soon replaced RFLP analysis and advanced to become the gold standard in genetic identification. Meanwhile, STR multiplexes have been developed and made commercially available which simultaneously amplify up to 30 STR loci from as little as 15 cells or fewer. The enormous information content that comes with the large variety of observed STR genotypes allows for genetic individualisation (with the exception of identical twins). Carefully selected core STR loci form the basis of intelligence-led DNA databases that provide investigative leads by linking unsolved crime scenes and criminals through their matched STR profiles. Nevertheless, the success of modern DNA fingerprinting depends on the availability of reference material from suspects. In order to provide new investigative leads in cases where such reference samples are absent, forensic scientists started to explore the prediction of phenotypic traits from the DNA of the evidentiary sample. This paradigm change now uses DNA and epigenetic markers to forecast characteristics that are useful to triage further investigative work. So far, the best investigated externally visible characteristics are eye, hair and skin colour, as well as geographic ancestry and age. Information on the chronological age of a stain donor (or any sample donor) is elemental for forensic investigations in a number of aspects and has, therefore, been explored by researchers in some detail. Among different methodological approaches tested to date, the methylation-sensitive analysis of carefully selected DNA markers (CpG sites) has brought the most promising results by providing prediction accuracies of ±3-4 years, which can be comparable to, or even surpass those from, eyewitness reports. This mini-review puts recent developments in age estimation via (epi)genetic methods in the context of the requirements and goals of forensic genetics and highlights paths to follow in the future of forensic genomics.
Topics: Aging; CpG Islands; DNA Fingerprinting; Databases, Nucleic Acid; Epigenomics; Forensic Genetics; Humans; Microsatellite Repeats
PubMed: 29393215
DOI: 10.1159/000486239 -
Medical Principles and Practice :... 2019Unlike DNA fingerprinting, which scores for differences in the genome that are phenotype neutral, epigenetic variations are gaining importance in forensic... (Review)
Review
Unlike DNA fingerprinting, which scores for differences in the genome that are phenotype neutral, epigenetic variations are gaining importance in forensic investigations. Methylation of DNA has a broad range of effects on the lifestyle, health status, and physical appearance of individuals. DNA methylation profiling of forensic samples is useful in determination of the cell or tissue type of the DNA source and also for estimation of age. The quality and quantity of the biosample available from the crime scene limits the possible number of DNA methylation tests and the selection of the technology that can be used. Several techniques have been used for DNA methylation analysis for epigenetic investigations of forensic biological samples. However, novel techniques are needed for multiplex analysis of epigenetic markers as the techniques that are currently available require a large amount of high-quality DNA and are also limited in their multiplexing capacities that are often insufficient to fully resolve a forensic query of interest.
Topics: DNA Fingerprinting; Epigenomics; Forensic Genetics; Humans
PubMed: 30893697
DOI: 10.1159/000499496 -
Clinical Microbiology Reviews Apr 2000DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform... (Review)
Review
DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies.
Topics: DNA Fingerprinting; DNA Probes; DNA, Fungal; Fungi; Humans; Mycological Typing Techniques; Mycoses; Polymerase Chain Reaction; Random Amplified Polymorphic DNA Technique; Software
PubMed: 10756003
DOI: 10.1128/CMR.13.2.332 -
Fa Yi Xue Za Zhi Oct 2021
Topics: Chromosomes, Human, Y; DNA Fingerprinting; Humans; Male
PubMed: 35191255
DOI: 10.12116/j.issn.1004-5619.2020.500705 -
Genes Nov 2021Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to... (Review)
Review
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.
Topics: DNA; DNA Fingerprinting; Forensic Genetics; Humans; Specimen Handling
PubMed: 34828372
DOI: 10.3390/genes12111766 -
International Journal of Molecular... Dec 2022Collection and interpretation of "touch DNA" from crime scenes represent crucial steps during criminal investigations, with clear consequences in courtrooms. Although... (Review)
Review
Collection and interpretation of "touch DNA" from crime scenes represent crucial steps during criminal investigations, with clear consequences in courtrooms. Although the main aspects of this type of evidence have been extensively studied, some controversial issues remain. For instance, there is no conclusive evidence indicating which sampling method results in the highest rate of biological material recovery. Thus, this study aimed to describe the actual considerations on touch DNA and to compare three different sampling procedures, which were "single-swab", "double-swab", and "other methods" (i.e., cutting out, adhesive tape, FTA paper scraping), based on the experimental results published in the recent literature. The data analysis performed shows the higher efficiency of the single-swab method in DNA recovery in a wide variety of experimental settings. On the contrary, the double-swab technique and other methods do not seem to improve recovery rates. Despite the apparent discrepancy with previous research, these results underline certain limitations inherent to the sampling procedures investigated. The application of this information to forensic investigations and laboratories could improve operative standard procedures and enhance this almost fundamental investigative tool's probative value.
Topics: Touch; DNA Fingerprinting; DNA; Specimen Handling
PubMed: 36555182
DOI: 10.3390/ijms232415541 -
Astrobiology Jul 2018Most strategies for life detection rely upon finding features known to be associated with terran life, such as particular classes of molecules. But life may be vastly...
Most strategies for life detection rely upon finding features known to be associated with terran life, such as particular classes of molecules. But life may be vastly different on other planets and moons, particularly as we expand our efforts to explore ocean worlds like Europa and Enceladus. We propose a new concept for life detection that harnesses the power of DNA sequencing to yield intricate informatics fingerprints, even for life that is not nucleic acid-based. The concept is based on the fact that folded nucleic acid structures (aptamers) have been shown to be capable of binding a wide variety of compounds, whether inorganic, organic, or polymeric, and irrespective of being from a biotic or abiotic source. Each nucleic acid sequence can be thought of as a code, and a combination of codes as a "fingerprint." Over multiple analytes, the "fingerprint" of a non-terran sample can be analyzed by chemometric protocols to provide a classifier of molecular patterns and complexity. Ultimately the chemometric fingerprints of living systems, which may differ significantly from nonliving systems, could provide an empirical, agnostic means of detecting life. Because nucleic acids are exponentially amplified by the polymerase chain reaction, even very small input signals could be translated into a robust readable output. The derived sequences could be identified by a small, portable sequencing device or by capture and optical imaging on a DNA microarray. Without presupposing any particular molecular framework, this agnostic approach to life detection could be used from Mars to the far reaches of the Solar System, all within the framework of an instrument drawing little heat and power. Key Words: Agnostic biosignatures-Astrobiology-Chemometrics-DNA sequencing-Life detection-Proximity ligation assay. Astrobiology 18, 915-922.
Topics: DNA; DNA Fingerprinting; Exobiology; Extraterrestrial Environment; Life; Planets; Sequence Analysis, DNA
PubMed: 29634318
DOI: 10.1089/ast.2017.1712 -
Forensic Science, Medicine, and... Mar 2023Several commercially available quantitative real-time PCR (qPCR) systems enable highly sensitive detection of human DNA and provide a degradation index (DI) to assess...
Several commercially available quantitative real-time PCR (qPCR) systems enable highly sensitive detection of human DNA and provide a degradation index (DI) to assess DNA quality. From routine casework in forensic genetics, it was observed that DNA degradation in forensic samples such as blood samples stored under sub-optimal conditions leads to visible effects in multiplex analyses of short tandem repeat markers (STRs) due to decreased amplification efficiencies in longer amplicons. It was further noticed that degradation indices often remain below the value that is considered to be critical. Thus, the aim of this work was to systematically analyze this effect and to compare conventional qPCR assays with a modified qPCR approach using uracil DNA glycosylase (UNG) and DNA quality assessment methods based on electrophoresis. Blood samples were stored at three different storage temperatures for up to 316 days. Significantly increased DNA recovery was observed from samples stored at high temperatures (37 °C) compared samples stored at room temperature and 4 °C. We observed typical effects of degradation in STR analyses but no correlation between DI and storage time in any of the storage conditions. Adding UNG slightly increased the sensitivity of detecting DNA degradation in one of the qPCR kits used in this study. This observation was not confirmed when using a second qPCR system. Electrophoretic systems did also not reveal significant correlations between integrity values and time. Methods for detecting DNA degradation are usually limited to the detection of DNA fragmentation, and we conclude that degradation affecting forensic STR typing is more complex.
Topics: Humans; DNA; DNA Damage; DNA Degradation, Necrotic; DNA Fingerprinting; Microsatellite Repeats; Real-Time Polymerase Chain Reaction; Blood Specimen Collection
PubMed: 36355320
DOI: 10.1007/s12024-022-00549-3 -
Fa Yi Xue Za Zhi Jun 2023To investigate the efficacy of different numbers of microhaplotype (MH) loci and the introduction of different reference samples on the identification of full sibling,...
OBJECTIVES
To investigate the efficacy of different numbers of microhaplotype (MH) loci and the introduction of different reference samples on the identification of full sibling, half sibling and differentiation between full sibling and half sibling kinships, and to explore the effect of changing mutation rate on sibling testing.
METHODS
First, a family map involving three generations was established, and four full sibling identification models, five half sibling identification models and five models distinguishing full and half siblings were constructed for different reference samples introduced. Based on the results of the previous study, two sets of nonbinary SNP-MH containing 34 and 54 loci were selected. Based on the above MH loci, 100 000 pairs of full sibling . unrelated individuals, 100 000 pairs of half sibling . unrelated individuals and 100 000 pairs of full sibling . half sibling were simulated based on the corresponding sibling kinship testing models, and the efficacy of each sibling kinship testing model was analyzed by the likelihood ratio algorithm under different thresholds. The mutant rate of 54 MH loci was changed to analyze the effect of mutation rate on sibling identification.
RESULTS
In the same relationship testing model, the systematic efficacy of sibling testing was positively correlated with the number of MH loci detected. With the same number of MH loci, the efficacy of full sibling testing was better than that of uncle or grandfather when the reference sample introduced was a full sibling of A, but there was no significant difference in the identification efficacy of the four reference samples introduced for full sibling and half sibling differentiation testing. In addition, the mutation rate had a slight effect on the efficacy of sibling kinship testing.
CONCLUSIONS
Increasing the number of MH loci and introducing reference samples of known relatives can increase the efficacy of full sibling testing, half sibling testing, and differentiation between full and half sibling kinships. The level of mutation rate in sibling testing by likelihood ratio method has a slight but insignificant effect on the efficacy.
Topics: Humans; Siblings; Polymorphism, Single Nucleotide; DNA Fingerprinting
PubMed: 37517018
DOI: 10.12116/j.issn.1004-5619.2023.530101 -
Yakugaku Zasshi : Journal of the... 2019As criminal cases have become more complicated, Japan's law enforcement officials are promoting the use of more sophisticated technologies, such as DNA analysis, in the... (Review)
Review
As criminal cases have become more complicated, Japan's law enforcement officials are promoting the use of more sophisticated technologies, such as DNA analysis, in the course of criminal investigations in order to verify facts with objective evidence. The primary DNA analysis method employed by law enforcement officials is short tandem repeat (STR) analysis, a method for identifying individuals utilizing individual differences in the number of repeat units of characteristic DNA sequences. Presently, STR analysis can discriminate between individuals with the probability of one in approximately 4.7 trillion, even when the DNA profile is the most common type among the Japanese population. In every prefectural police department, members of criminal investigation laboratories, who were trained and certified by the Training Center of Forensic Science at the National Research Institute of Police Science, perform STR analysis. Forensic DNA analysis plays an important role not only in criminal investigations but also following large-scale disasters, to aid in individual identification. The accuracy of DNA typing is increasing with the availability of STR typing kits that can examine more loci than conventional kits. However, it remains difficult for DNA analysis to identify individuals with only small amounts of samples, old samples, or mixed samples. New methods for handling these problematic samples are required. Here, we review current investigative techniques and challenges of DNA analysis, and focus on the latest research for solutions to these challenges.
Topics: Crime; DNA Fingerprinting; Forensic Anthropology; Humans; Japan; Microsatellite Repeats; Sequence Analysis, DNA
PubMed: 31061341
DOI: 10.1248/yakushi.18-00166-6