Figure 2 - uploaded by Peter Gill
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An example of trisomy showing three different alleles. D21S11 trisomy or translocation in the lower pane. Note that the bands are equivalent in size. Allelic ladder in the upper pane. Amp Fl STR SGM Plus system.
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The analysis of short tandem repeat (STR) DNA sequences is of fundamental importance to forensic science because they have become the recognized standard in constructing national public databases. Consequently, considerable effort has been expended in developing multiplexed (one tube) reactions that analyze several loci in combination. The implemen...
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Citations
... Both of these methods have shown promise in improving the success rate of nDNA profiling from degraded samples. These advancements are essential to improve the reliability and accuracy of forensic investigations (Li 2008;Gill, 2002). ...
Background
DNA (deoxy-ribonucleic acid) is a fundamental molecule housing genetic information crucial for forensic casework. However, its integrity is compromised over time due to degradation, affecting living and deceased organisms. Understanding the factors and mechanisms of DNA degradation is vital across scientific disciplines.
Main body
DNA degradation is a dynamic process influenced by factors like temperature, humidity, and ultraviolet radiation. The post-mortem interval affects organisms differently, and mechanisms such as hydrolysis, oxidation, and depurination impact DNA structural integrity. In forensic casework, DNA degradation poses challenges because degraded DNA samples can be difficult to analyze. Despite these challenges, DNA degradation has become an invaluable asset in forensic science. Fragmented DNA aids in historical identification and archaeological investigations. Additionally, DNA degradation helps estimate the time since death, assisting investigators in criminal timelines. Forensic experts use degradation patterns to deduce environmental conditions affecting a body, aiding crime scene reconstruction. In criminal investigations, advancements in DNA recovery, like next-generation sequencing, enable the analysis of severely degraded samples, enhancing the identification of suspects and victims.
Conclusion
DNA degradation, despite its challenges, is a potent tool in forensic science. Understanding the factors and mechanisms influencing DNA degradation is essential for its effective utilization in criminal casework. With ongoing advancements in forensic techniques and technologies, the reliability and utility of degraded DNA analysis are steadily increasing, helping to bring resolution to complex criminal cases and uncovering hidden clues in forensic investigations.
... The current gold standard for forensic DNA profiling is the sizing of a limited set of carefully chosen short tandem repeat (STR) markers, for example, a commonly used panel of 23 autosomal STR markers, based on a capillary electrophoresis (CE) platform [2,3]. This method has been found to be very efficient for analysing profiles of single-source DNA or a simple two-person DNA mixture [4,5]. However, an interpretation of more complex DNA mixtures from three or more contributors has been challenging, which is mainly due to the production of confounding stutter products, allele dropout during STR amplification and insufficient sensitivity of the CE measurements [6][7][8]. ...
The need to identify a missing person (MP) through kinship analysis of DNA samples found at a crime scene has become increasingly prevalent. DNA samples from MPs can be severely degraded, contain little DNA and mixed with other contributors, which often makes it difficult to apply conventional methods in practice. This study developed a massively parallel sequencing-based panel that contains 1661 single-nucleotide polymorphisms (SNPs) with low minor allele frequencies (MAFs) (averaged at 0.0613) in the Chinese Han population, and the strategy for relationship inference from DNA mixtures comprising different numbers of contributors (NOCs) and of varying allele dropout probabilities. Based on the simulated dataset and genotyping results of 42 artificial DNA mixtures (NOC = 2-4), it was observed that the present SNP panel was sufficient for balanced mixtures when referenced to the closest relatives (parents/offspring and full siblings). When the mixture profiles suffered from dropout, incorrect assignments were markedly associated with relatedness, NOC and the dropout level. We, therefore, indicate that SNPs with low MAFs could be reliably interpreted for MP identification through the kinship analysis of complex DNA mixtures. Further studies should be extended to more possible scenarios to test the feasibility of this present approach.
... На відміну від України, закордонні автори, навпаки, неодноразово висловлювались з приводу власного бачення минулого, теперішнього та майбутнього галузі криміналістичного ДНК-аналізу. Зокрема, це праці П. Гілла, Д. Батлера, Л. Роевера, А. Карраседо та багатьох інших авторів, які розвивали різні технології криміналістичного ДНК-аналізу та проводили наукові огляди з його актуальних проблем [4][5][6][7]. ...
... The current gold standard for forensic DNA profiling is the sizing of a limited set of carefully chosen short tandem repeat (STR) markers, for example, a commonly used panel of 23 autosomal STR markers, based on a capillary electrophoresis (CE) platform [2,3]. This method has been found to be very efficient for analysing profiles of single-source DNA or a simple two-person DNA mixture [4,5]. However, an interpretation of more complex DNA mixtures from three or more contributors has been challenging, which is mainly due to the production of confounding stutter products, allele dropout during STR amplification and insufficient sensitivity of the CE measurements [6][7][8]. ...
In forensic applications, there is an increasing demand for the analysis of DNA profiles arising from missing person identification (MPI) cases. A specific DNA profile may originate from a single source or more than one contributor (i.e., a DNA mixture). When direct references are not available, indirect relative references can be used to identify missing persons by kinship analysis. As a novel kind of multiallelic marker, microhaplotypes have proven promising for relatedness determination and mixture deconvolution. Herein, we developed a large panel of 185 microhaplotype markers and demonstrated its application in different scenarios of relationship inference through a simulation study and real pedigree analysis, combined with probabilistic genotyping models for data interpretation. Based on single-source profiles, it was shown that the present microhaplotype panel was sufficient for pairwise close relative testing (parent/child, full-sibling and 2nd-degree relative). For more distant relatives (3rd-degree relatives), there was a clear improvement when data from one well-chosen extra relative were available. We further sought to evaluate the theoretical systematic effectiveness and actual performance of microhaplotype markers in identifying the contribution of a missing pedigree member to a two-person mixture (as a minor donor). It was observed that 100% correct assignments were made in the balanced mixtures (with no dropout) when referenced to close relatives. When the mixture profiles suffered from dropout, incorrect assignments of minor donors were markedly associated with relatedness and the dropout level. Meanwhile, the studied scenarios generally exhibited zero or very low false-positive rates, indicating a low probability of incorrectly assigning an unrelated contributor as a close relative of the reference. Our results indicate that microhaplotype data can be reliably interpreted for identifying missing persons through kinship analysis based on DNA profiles of single-source samples or two-person mixtures. Furthermore, this study could be extended to more complex scenarios, such as determining the relatedness of contributors in (or among) mixed DNA profiles, if combined with different statistical frameworks.
... Contaminating DNA may be introduced to a sample by the first responding officers, rescue workers, or crime scene investigators present at the crime scene, archaeologists during excavations or later by laboratory personnel during DNA analysis [5][6][7]. Contamination may also originate from other samples processed at the same laboratory (cross-contamination) [6,8] or even from disposables and consumables contaminated during manufacturing [9,10]. ...
... Several preventive measures should be taken to reduce the risk of contamination in order to assure a high quality of DNA profiling results. Contamination is monitored by establishing elimination databases with DNA profiles from staff [11], periodic wipe tests, and the use of no template control (NTC) reactions [8]. Moreover, personal protective clothing, disposable consumables, aerosol resistant tips, and dedicated instruments are used to prevent the introduction of contaminating DNA into the laboratory environment and casework samples. ...
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.
... Així, la identifi cació genètica, tenint com a base les dades mitocondrials per la seva relativament fàcil adquisició en aquell moment, es va completar amb l'estudi de marcadors nuclears. Concretament, es van fer servir els marcadors habituals de les identifi cacions forenses, els STR autosòmics (Gill 2002). Els STR són fragments d'ADN en els quals un nombre petit de nucleòtids, habitualment quatre en l'àmbit forense, es repeteixen en tàndem (per exemple, ACTT, ACTT... fi ns a N repeticions). ...
The Generalitat de Catalunya between 2006 and 2016 commisioned the excavation of a series of mass graves from the Spanish Civil War and subsequent Franco dictatorship to identify the victims. The final step of this process consisted of genetic analyses to both ascertain or confirm the identifications of the victims. In spite of the fact that certain could be identified, significant challenges remain. The main obstacles are the poor state of the remains, and consequently the genetic material, and the lack of living relatives, specially first-degree relatives. These problems are stil valid today and are responsible for the current low rate of identification. Genetic analyses are only part of the strategy of identification so as to be able to return the remains of the victims to their families. This task must be carried out in the framework of an interfisciplinary approach combining documentary, antemortem, ane in-depth antropological research.
... STRs are used as the foundation of DNA databases globally because of their high polymorphism and their ability to generate results from minimal quantity of template using Polymerase Chain Reaction (PCR). As the information updated in databases is large in size and also continues to grow progressively, it is crucial that the potential number of adventitious matches is kept to a minimum [33][34][35]. The commercially available PCR amplification kit AmpFLSTR™ Identifiler™ Plus provides increased efficiency and greater sensitivity for processing of DNA samples for databasing and forensic casework [21]. ...
Identifying missing persons and unidentified dead bodies is a well-documented global problem in recent years. To curb this issue, countries such as the USA, UK, and Australia already have well-established DNA databases. Considering the alarming number of unidentified/unclaimed dead bodies reported in India every year, it is evident that the current practices are not sufficient to establish their identities. Forensic medicine professionals are ethically, morally, and dutybound to collect information about missing and unidentified persons and work with the government agencies to determine their identity. Concerning the social and public interest, we have developed the first-ever identification portal and DNA database of unidentified dead bodies autopsied at the Department of Forensic Medicine and Toxicology, AIIMS, New Delhi, India. After the investigation officer's informed consent, biological samples from unidentified dead bodies and a detailed phenotypic description, anthropological data and other visual characteristics of the deceased are recorded at the time of autopsy. This information is uploaded on our database which is available for public access, and the genotypic information generated through STR analysis is only available for internal usage. Claimants (biological relatives) may browse through the URL (https://umid-aiims.icmr.org.in/), and if they wish to claim an unidentified dead body, they may approach as per the given guidelines. The DNA profiles generated include a total of 16 STRs (15 autosomal tetranucleotide microsatellite STRs and 1 Sex Chromosome Specific STR). The claimant's STR profile is run through the questioned database to look for a potential match. If positive, the investigating officer of that particular case is informed for further necessary action. Until December 2020, our database consisted the information of 255 individuals and two unidentified cadavers were identified. This project's success can also lead to a pioneering National DNA database of unidentified and missing persons in India.
... Furthermore, DNA profiling unlike other, forensic evidence can be collected easily and sustains for a long thereby increasing chances of accurate analysis by manifold. It has become an important method for human identification by introducing the study of microsatellite regions -Short Tandem Repeats (STR) Loci in criminal and civil cases [13][14][15]. The STR fragments are separated and detected by using capillary electrophoresis. ...
... Short tandem repeats (STRs) are short tandemly repeated DNA sequences composed of repetitive units of 1-6 bp [1]. STRs are widespread throughout the human genome and serve as widely used polymorphism markers in forensic science [1,2]. For forensic casework, ideal STR loci should generally have the following characteristics such as approximate fragments ranging from 100 to 500 bp, high heterozygosity, low stutter, a low mutation rate, and so on [3,4]. ...
... In order to filter STRsearch calls to obtain only highquality genotypes, a base classifier using the XGBoost Reference sequence repeat region sequence structure summary based on the most up-to-date forensic STR sequence guide 2 Alleles correction according to the stutter ratio, which is 0.5 in this study. '-', not applicable algorithm [35] was built. ...
Background:
Short tandem repeats (STRs) are important polymorphism makers for human identification and kinship analyses in forensic science. With the continuous development of massively parallel sequencing (MPS), more laboratories have utilized this technology for forensic applications. Existing STR genotyping tools, mostly developed for whole-genome sequencing data, are not effective for MPS data. More importantly, their backward compatibility with the conventional capillary electrophoresis (CE) technology has not been evaluated and guaranteed.
Results:
In this study, we developed a new end-to-end pipeline called STRsearch for STR-MPS data analysis. The STRsearch can not only determine the allele by counting repeat patterns and INDELs that are actually in the STR region, but it also translates MPS results into standard STR nomenclature (numbers and letters). We evaluated the performance of STRsearch in two forensic sequencing datasets, and the concordance with CE genotypes was 75.73 and 75.75%, increasing 12.32 and 9.05% than the existing tool named STRScan, respectively. Additionally, we trained a base classifier using sequence properties and used it to predict the probability of correct genotyping at a given locus, resulting in the highest accuracy of 96.13%.
Conclusions:
All these results demonstrated that STRsearch was a better tool to protect the backward compatibility with CE for the targeted STR profiling in MPS data. STRsearch is available as open-source software at https://github.com/AnJingwd/STRsearch.
... Los STRs están ubicados por toda la extensión del genoma humano, los ubicados en los cromosomas autosómicos y en el cromosoma Y han sido ampliamente utilizados en los laboratorios de genética forense debido a las características y patrones hereditarios que estos poseen, a finales de la presente década se ha incrementado la investigación de STRs del cromosoma X (STR-X) para ser empleados en el ámbito forense, debido al beneficio de su empleo en casos de vínculos biológicos complejos donde el uso de los STRs autosómicos y del cromosoma Y, aportan información irrelevante o no es posible su aplicación [3][4][5][6] . Como en el resto del genoma humano, los marcadores STRs son abundantes a lo largo del cromosoma X con una densidad comparable a los STRs autosómicos. ...
Justificación: Las repeticiones cortas en tándem (STRs) están distribuidos por toda la extensión del genoma humano, los ubicados en los cromosomas autosómicos y en el cromosoma Y han sido ampliamente utilizados en los laboratorios de genética forense debido a las características y patrones hereditarios que estos poseen. Objetivo: A fin de caracterizar y determinar parámetros de interés forense en secuencias de tipo STR del cromosoma X (DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08 y DXS7423) en la población del Estado Zulia. Metodología: Se eligieron 108 individuos (130 cromosomas X), cuyos ADN se amplificaron mediante la reacción en cadena de la polimerasa, los fragmentos se separaron por electroforesis capilar y los alelos reportados con respecto a la escalera alélica. Resultados: El contenido de información polimórfica demostró ser mayor de 0,5 en todos los microsatélites y el poder de discriminación acumulado fue de 0,99999997 en mujeres y 0,99999816 en hombres. Conclusiones: Los datos demuestran que los microsatélites del cromosoma X analizados son lo suficientemente informativos como para ser utilizados en casos de vínculos biológicos complejos y la identificación humana.
