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Tillmar, Andreas. "Populations and Statistics in Forensic Genetics." Doctoral thesis, Linköpings universitet, Institutionen för klinisk och experimentell medicin, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-54742.
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DNA has become a powerful forensic tool for solving cases such as linking a suspect to a crime scene, resolving biological relationship issues and identifying disaster victims. Traditionally, DNA investigations mainly involve two steps; the establishment of DNA profiles from biological samples and the interpreta-tion of the evidential weight given by theses DNA profiles. This thesis deals with the latter, with focus on models for assessing the weight of evidence and the study of parameters affecting these probability figures. In order to calculate the correct representative weight of DNA evidence, prior knowledge about the DNA markers for a relevant population sample is required. Important properties that should be studied are, for example, how frequently certain DNA-variants (i.e. alleles) occur in the population, the differences in such frequencies between subpopulations, expected inheritance patterns of the DNA markers within a family and the forensic efficiency of the DNA markers in casework. In this thesis we aimed to study important population genetic parameters that influence the weight of evidence given by a DNA-analysis, as well as models for proper consideration of such parameters when calculating the weight of evi-dence in relationship testing. We have established a Swedish frequency database for mitochondrial DNA haplotypes and a haplotype frequency database for markers located on the X-chromosome. Furthermore, mtDNA haplotype frequencies were used to study the genetic variation within Sweden, and between Swedish and other European populations. No genetic substructure was found in Sweden, but strong similari-ties with other western European populations were observed. Genetic properties such as linkage and linkage disequilibrium could be im-portant when using X-chromosomal markers in relationship testing. This was true for the set of markers that we studied. In order to account for this, we pro-posed a model for how to take linkage and linkage disequilibrium into account when calculating the weight of evidence provided by X-chromosomal analysis. Finally, we investigated the risk of erroneous decisions when using DNA in-vestigations for family reunification. We showed that the risk is increased due to uncertainties regarding population allele frequencies, consanguinity and compet-ing close relationship between the tested individuals. Additional information and the use of a refined model for the alternative hypotheses reduced the risk of making erroneous decisions. In summary, as a result of the work on this thesis, we can use mitochondrial DNA and X-chromosome markers in order to resolve complex relationship in-vestigations. Moreover, the reliability of likelihood estimates has been increased by the development of models and the study of relevant parameters affecting probability calculations.
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Santos, Leonardo Soriano de Mello 1976. "Viabilidade da utilização de amostras biologicas obtidas de dentes humanos para obtenção de perfis geneticos de DNA." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/290762.
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Orientadores: Eduardo Daruge Junior, Darcy de Oliveira ToselloDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba
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Resumo: Alguns fatores relacionados ao estado e lugares que dentes humanos se encontram, nos que diz respeito a estes enquanto amostras com finalidade forense, ainda constituem desafio ao que tange o uso dos mesmos como material para obtenção de perfis genéticos de DNA. Este estudo visou comparar a extração de DNA feita a partir de dentes humanos com a extração por meios de amostras de sangue fixadas em papel FTA® utilizadas como grupo controle, de maneira a comparar os alelos mapeados e definir se os dentes constituem nestas circunstâncias, fonte viável de amostras para obtenção de perfis genéticos, comparando os protocolos. Dezoito participantes foram abordados e, aceitaram participar da pesquisa por meio de TCLE's, doaram voluntariamente amostras de sangue e os elementos dentários terceiros molares superiores direitos, estes indicados para exodontia por outros profissionais. Verificou-se que os dentes humanos constituíram fontes viáveis de acordo com a análise estatística realizada (Teste de Poisson), onde p<0,0001, entretanto quando comparado com o protocolo de extração de material genético através do sangue, deixa de ser viável devido ao número de passos necessários para a obtenção dos resultados. Ainda, 78,125% dos alelos possíveis de serem mapeados, o foram com sucesso
Abstract: Several factors related to how and where human teeth are found in forensic cases still a challenge to obtain genetic DNA profiles, as using theses elements as source for genetic material. This study aimed to compare the DNA extraction done through blood stains in FTA® paper cards, used as control group, and compare the mapped alleles from these to ones extracted from human teeth samples, as the simplicity of theses protocols when in comparison. Eighteen participants were convinced to join this study. Blood samples and superior right third molars (element 18) were donated. As result, teeth provided good sources of biologic sampling to obtain genetic profiles when analyzed by Poisson statistic analysis (p<0,0001), however, when compared to genetic material extraction protocol by blood, teeth analysis is no longer viable due to extensive laboratorial steps in order to gain the same results. Also 78,125% of the possible locci to be mapped and amplified were indeed
Mestrado
Odontologia Legal e Deontologia
Mestre em Biologia Buco-Dental
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Gettings, Katherine Butler. "Forensic Ancestry and Phenotype SNP Analysis and Integration with Established Forensic Markers." Thesis, The George Washington University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3590467.
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When an evidential DNA profile does not match identified suspects or profiles from available databases, further DNA analyses targeted at inferring the possible ancestral origin and phenotypic characteristics of the perpetrator could yield valuable information. Single Nucleotide Polymorphisms (SNPs), the most common form of genetic polymorphisms, have alleles associated with specific populations and/or correlated to physical characteristics. With this research, single base primer extension (SBE) technology was used to develop a 50 SNP assay designed to predict ancestry among the primary U.S. populations (African American, East Asian, European, and Hispanic/Native American), as well as pigmentation phenotype. The assay has been optimized to a sensitivity level comparable to current forensic DNA analyses, and has shown robust performance on forensic-type samples. In addition, three prediction models were developed and evaluated for ancestry in the U.S. population, and two models were compared for eye color prediction, with the best models and interpretation guidelines yielding correct information for 98% and 100% of samples, respectively. Also, because data from additional DNA markers (STR, mitochondrial and/or Y chromosome DNA) may be available for a forensic evidence sample, the possibility of including this data in the ancestry prediction was evaluated, resulting in an improved prediction with the inclusion of STR data and decreased performance when including mitochondrial or Y chromosome data. Lastly, the possibility of using next-generation sequencing (NGS) to genotype forensic STRs (and thus, the possibility of a multimarker multiplex incorporating all forensic markers) was evaluated on a new platform, with results showing the technology incapable of meeting the needs of the forensic community at this time.
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Nilsson, Martina. "Mitochondrial DNA in Sensitive Forensic Analysis." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7458.
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Andréasson, Hanna. "Sensitive Forensic DNA Analysis : Application of Pyrosequencing and Real-time PCR Quantification." Doctoral thesis, Uppsala University, Department of Genetics and Pathology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5775.
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The field of forensic genetics is growing fast and the development and optimisation of more sensitive, faster and more discriminating forensic DNA analysis methods is highly important. In this thesis, an evaluation of the use of novel DNA technologies and the development of specific applications for use in forensic casework investigations are presented.
In order to maximise the use of valuable limited DNA samples, a fast and user-friendly Real-time PCR quantification assay, of nuclear and mitochondrial DNA copies, was developed. The system is based on the 5’ exonuclease detection assay and was evaluated and successfully used for quantification of a number of different evidence material types commonly found on crime scenes. Furthermore, a system is described that allows both nuclear DNA quantification and sex determination in limited samples, based on intercalation of the SYBR Green dye to double stranded DNA.
To enable highly sensitive DNA analysis, Pyrosequencing of short stretches of mitochondrial DNA was developed. The system covers both control region and coding region variation, thus providing increased discrimination power for mitochondrial DNA analysis. Finally, due to the lack of optimal assays for quantification of mitochondrial DNA mixture, an alternative use of the Pyrosequencing system was developed. This assay allows precise ratio quantification of mitochondrial DNA in samples showing contribution from more than one individual.
In conclusion, the development of optimised forensic DNA analysis methods in this thesis provides several novel quantification assays and increased knowledge of typical DNA amounts in various forensic samples. The new, fast and sensitive mitochondrial DNA Pyrosequencing assay was developed and has the potential for increased discrimination power.
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Divne, Anna-Maria. "Evaluation of New Technologies for Forensic DNA Analysis." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5744.
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Reid, Kate Megan. "Forensic human identification: Generating Y-STR data for the South African population." Master's thesis, Faculty of Health Sciences, 2018. http://hdl.handle.net/11427/30060.
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Salt River Mortuary (SRM), Cape Town, investigates ~3500 cases of unnatural death annually, with an apparent burden of unclaimed bodies. A retrospective review was first undertaken to assess the number of these individuals who remained unidentified. Medicolegal records were examined (2010-2017), and ~9% of cases remained unidentified each year. DNA analysis was performed in 23.5% of cases. At the time of this study, unidentified bodies were in storage for up to two years, pending pauper burial. DNA profiling assists forensic human identification, and the analysis of markers on the Y-chromosome has particular importance in kinship analysis. To evaluate the statistical probability of DNA profiles matching between samples, reference data from the background population is required. Such data for the Y-chromosome is lacking for some populations groups in South Africa (SA). As such this study aimed to generate Y-chromosome data relevant to SA. Second to this, the obtainability of DNA profiles from unidentified decedents at SRM, prior to pauper burial, was investigated. Biological samples were obtained from 653 SA individuals (living: n=480; deceased: n=173) belonging to four major population groups. Following internal validation, samples were processed using the Promega PowerPlex® Y23 System. A cohort-representative subset of DNA profiles were also generated using the forensically validated Next Generation Sequencing (NGS) assay on the MiSeq FGx™ system, to assess concordance. Statistical analysis was performed using Arlequin and STATA packages. Full DNA profiles (i.e. haplotypes) were obtained from 626 samples (African: n=183; Coloured: n=170; Indian/Asian: n=111; White: n=162), with 599 haplotypes being unique to a single individual. Following optimisation, haplotypes were obtained from >99% and 85% of living and deceased individuals, respectively. Haplotypes were generated from numerous individuals stored for over one year, and DNA profile quality was not associated with time between death declaration and sample collection. NGS results confirmed the presence of one micro-variant and resolved allele-calling in five instances where the capillary electrophoresis assay was incorrect. Thus, concordance was observed in 98% of loci reviewed. Overall, haplotypes were successfully obtained for four different SA population groups, including refrigerated decedents, even 887 days after death declaration. This demonstrates that DNA profiling can be successful for decedents and efforts should be made to store DNA profiles for the possibility of familial searching and identification, even after burial. Identification of the multitude of unclaimed bodies at forensic facilities nationwide holds immense value for living family members, and provides closure for the acceptance of death and life thereafter.
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Tully, Gillian. "DNA profiling for forensic identification : evaluation of polymerase chain reaction methods." Thesis, Cardiff University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264882.
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Bashir, Majid. "Application of autosomal INDELs as a forensic tool in Qatar." Thesis, University of Central Lancashire, 2016. http://clok.uclan.ac.uk/15480/.
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Short tandem Repeats (STRs) are the most commonly genetic markers used in forensic human identification. However, in some cases they are not able to yield complete profiles because of DNA degradation and/or inhibition. The STR profiling of the degraded/inhibited DNA samples can result in allelic drop-outs and even no profile at all. Alternatively, single nucleotide polymorphisms (SNPs) can be used to address the issues of DNA degradation and inhibition due to their smaller amplicons. But their use in regular forensic case work is limited due to additional steps (sequencing based) and time consuming process. To bridge the gap between STRs and SNPs by combining their characteristics, another type of genetic marker, insertion deletion polymorphisms (INDELs), offer an effective way to analyze challenged DNA sample (degraded and inhibited ones). INDELs have short amplicons, low mutation rates, no stutter peaks and are analyzed using the same equipment and protocols as STR polymorphisms. In this study, the forensic efficiency of 30 autosomal INDELs contained within the Qiagen™ Investigator™ DIPplex kit were tested by using 500 samples from individuals belonging to five different nationalities (Qatari, Pakistani, Sudanese, Tunisian and Yemeni) based in Qatar. Population indices and forensic parameters were calculated. The results showed no significant deviation from Hardy-Weinberg Equilibrium and no evidence of linkage disequilibrium for all of 30 markers was found after applying Bonferroni’s correction (P < 0.00166). The Combined Power of Discrimination (CPD) for the 30 INDEL loci was 0.9999999 for all of five populations which shows that these 30 markers are very efficient and suitable for forensic casework. The Combined Probability of Match (CPM) was calculated in the order of 10-13 which is a satisfactory value for forensic purposes. In addition to assess forensic efficiency of 30 autosomal INDELs, an effort was also made to derive ancestry information by using different statistical systems (Arlequin, Snipper and STRUCTURE). The results indicated that 30 INDELs contained in Qiagen™ Investigator® DIPplex kit, although useful for forensic identification, poorly differentiate five population groups of Qatar. The reason of failure in differentiating the populations, lies in the selection of INDEL markers, which were chosen for identification purpose (i.e. they have similar allele frequencies in different populations) rather than deriving the ancestry information (i.e. iii ancestry informative markers are chosen on the basis that their allele frequencies need to be different for different populations). In order to recover genetic information lost during DNA degradation, the concept of reduced sized PCR products (mini amplicons) has been developed. MiniFiler® kit (Applied Biosystems™) containing 8 mini-STRs (developed by re-designing the primers of 8 STRs contained in Identifiler Plus® kit) provide a possible solution of DNA degradation. By using similar mini-plex approach, a multiplex PCR assay for INDELs (named as mini-INDELs) has been developed in this research. A total of 14 autosomal INDEL markers were selected and short amplicons were designed for them keeping in view that they could perform efficiently on degraded samples. The multiplex of 14 INDELs was designed and optimized successfully in a single tube reaction. All the markers were amplified adequately with good peak balance and expected amplicon sizes. The sensitivity of mini-INDELs was found upto 0.03125 ng of genomic DNA with complete and balanced profile. The concordance between mini-INDELs kit and Qiagen™ Investigator™ DIPplex kit (for the common loci) was observed in 99.7% INDEL alleles. The efficiency of mini-INDELs PCR assay was also evaluated on a set of artificially prepared degraded and inhibited DNA samples. It is concluded that INDELs markers in general and mini-INDELs in specific, can be used as a useful tool in forensic case work and can also be employed in conjunction with STR typing as a complementary tool especially in those cases where low level of DNA and DNA degradation are suspected.
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Tau, Tiroyamodimo. "A forensic analysis of genetic variation in the Botswana population." University of the Western cape, 2016. http://hdl.handle.net/11394/5657.
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Philosophiae Doctor - PhDThis thesis has been placed under a long term embargo. Forensic and population genetic parameters were investigated in the Botswana population using autosomal and Y-chromosome short tandem repeat markers. AmpFlSTR Profiler plus markers were used to investigate the genetic diversity and forensic parameters in 773 individuals from Botswana from the reference database of the Botswana Police. The levels of polymorphism found using the AmpFlSTR Profiler Plus markers showed that the nine loci that make up the AmpFlSTR Profiler Plus can differentiate individuals for forensic casework in the Botswana population. AmpFlSTR Identifiler autosomal STR markers were used to investigate the population structure according to ethno-linguistics and geography 990 individuals from Botswana that serve as a reference database for the Botswana Police. Using pairwise genetic distances (Fst), analysis of molecular variance (AMOVA), factorial correspondence analysis (FCA), and the unsupervised Bayesian clustering method found in STRUCTURE and the landscape genetics software TESS, ethno-linguistics were found to have a greater influence on population structure than geography. The patterns of population structure found using these markers highlight the need for regional reference databases that include both ethnolinguistic and geographic location information. These markers have important potential for bio-anthropological studies as well as for forensic applications. The 17 Y-chromosomal short tandem repeats found in AmpFlSTR Y-filer and a highly discriminatory Y-STR genotyping system (the Y-STR 10-plex developed in the Forensics DNA Laboratory at the University of the Western Cape) were analysed in 249 unrelated male individuals from Botswana. Rst, multi-dimensional scaling (MDS) and AMOVA were used to investigate population differentiation in Botswana. The discrimination capacity (DC) was found to be higher using the Y-STR 10-plex as compared to the 17 markers in the Y-filer genotyping system. No geographic regional or ethnic differentiation was observed between the Northern and Southern regions of Botswana using both marker systems. Regional and ethnic variation can be useful in forensic working hypotheses. Cluster analysis using the highly discriminatory Y-STR 10-plex haplotypes may provide information about ancestry and haplogroup information.
National Research Foundation (NRF)
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Palmour, Nicole. "Forensic applications of molecular genetics: ethics and law to inform policy issues." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=66662.
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Molecular analysis of DNA variation has usurped the place of all earlier technologies in forensic identification of victims and suspects alike. Although the field of ethics has made attempts to cope with the plethora of available genetic information, especially in clinical application, there has been little scrutiny of emerging ethical issues in the forensic domain. Legal scholarship highlights some aspects of the emerging issues, with particular relevance to the challenges faced in court and those regarding individual liberties. The overall objective of this thesis was to evaluate the scientific validity, ethical acceptability and legal accountability of the forensic applications of molecular genetics. In particular, contemporary science has allowed us to access information far beyond what was originally anticipated, such that trace DNA can be obtained trivially from any individual. As a consequence, the scope and composition of existing DNA banks far exceeds the legislative mandate. Chapter 1 reviews the current legal standards for evidence and assesses the level of exactitude necessary for forensic DNA testing to meet evidentiary standards. An evaluation of current practices in DNA banking revealed adequate informed consent practices; the need for a re-examination of access to public health samples with attention to local population interests and the necessity for developing standardized guidelines for banking practices and uniform quality assessment measures (Chapter 2). Comparing current forensic and genomic markers revealed similar concordance and discordance rates with a slight performance advantage towards the forensic markers. The results indicate that multiple runs are necessary to ensure reliability (Chapter 3). A significant ethical issue arises from the forensic practice of surreptitious DNA sampling. This lack of transparency violates autonomy, threatens the legitimacy of the State's intL'analyse moléculaire des variations de l'ADN a supplanté toutes les technologies médicolégales antérieures d'identification des victimes et des suspects. Bien que le champ de l'éthique ait tenté de gérer la pléthore d'information génétique disponible, particulièrement dans les applications cliniques, il y a eu peu d'examen des enjeux éthiques émergeants dans le domaine médicolégal. La recherche juridique met en évidence certains aspects des enjeux émergeant avec une pertinence particulière pour les défis auxquels les tribunaux sont confrontés ainsi que les défis à l'égard des libertés individuelles.L'objectif général de cette thèse était d'évaluer la validité scientifique, l'acceptabilité éthique et la responsabilité légale dans les applications médicolégales de la génétique moléculaire. En particulier, la science contemporaine nous a permis d'accéder à des informations qui vont au-delà de ce qui était anticipé à l'origine si bien que des traces d'ADN peuvent être obtenues trivialement de tout individu. En conséquence, l'étendue et la composition des banques existantes d'ADN excèdent de loin le mandat législatif. Le premier chapitre revoit les standards légaux d'évidence et évalue le niveau d'exactitude nécessaire afin que les tests d'ADN médico-légaux rencontrent les standards d'évidence. Une évaluation des pratiques actuelles dans la mise en banque d'ADN a révélé des pratiques de consentement éclairé adéquate, le besoin de réexaminer l'accès aux échantillons de santé publique en portant l'attention aux intérêts des populations locales et la nécessité de développer des lignes directrices standardisées pour les pratiques de mise en banque et de mesures uniformes de l'évaluation de la qualité (chapitre 2). La comparaison des marqueurs médicolégaux actuels aux marqueurs génomiques a révélé des taux de concordance et de discord
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Ambrosio, Isabela Brunelli [UNESP]. "Análise de SNPs do DNA mitocondrial em indivíduos residentes no estado do Espírito Santo para aplicação na Identificação Humana." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/124408.
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000825088.pdf: 567086 bytes, checksum: 73ca882633cceb536b683b63c338096b (MD5)A identificação humana por meio do DNA constitui um dos produtos mais revolucionários da Genética Moderna, tornando-se uma ferramenta indispensável na investigação criminal. Essa identificação é baseada no perfil genético do indivíduo, pela combinação de diversos marcadores herdados de seus progenitores. Os marcadores são, geralmente,e diferenças nas sequências de DNA nuclear entre os indivíduos (polimorfismos). Em alguns casos, em que a análise do DNA nuclear não puder ser aplicada, a alternativa de maior sucesso é a análise do DNA mitocondrial (DNAmt). As mitocôndrias são organelas intracelulares de dupla membrana presentes em todas as células nucleadas de mamíferos, com genoma extracromossômico separado e distinto do genoma nuclear, o DNA mt. A maioria dos laboratórios que utilizam tipagem do DNAmt baseiam-se nos polimorfismos presentes na sequência de nucleotídeos na região não codificadora (também conhecida como região controle, hipervariável, ou D-loop) do DNAmt. No entanto, a classificação em alguns haplogrupos pode não ser possível com base em dados apenas da região controle. Assim, estudos sugerem a necessidade de tipagem adicional de polimorfismos de nucleotídeos únicos (SNPs) em outras regiões do DNAmt, em especial, nos casos onde não é possível diferenciar os indivíduos apenas pela análise da região hipervariável. Este trabalho teve como objetivo analisar, analisar 30 (trinta) SNPs do DNAmt em amostras de indivíduos não relacionados, nascidos e residentes no Estado do Espírito Santo, permitindo a classificação das mesmas em haplogrupos e complementando os dados de SNPs da região controle do DNAmt obtidos em trabalho anterior no laboratório, para posterior utilização em casos forense. De um total de 100 amostras, foram encontrados 19 haplogrupos e a população estudada foi classificada conforme sua origem em: 43% africana, 30% europeia...
Human identification through DNA is one of the most revolutionary products of Modern Genetics, making it an indispensable tool in criminal investigation. This identification is based on the genetic profile of the individual, the combination of several markers inherited from their parents. The markers are generally differences in nuclear and DNA sequences between individuals (polymorphisms). In some cases, the analysis of nuclear DNA cannot be applied, the most successful alternative is the analysis of mitochondrial DNA (mtDNA). Mitochondria are intracellular organelles with a double membrane present on all nucleated mammalian cells with separate and distinct extrachromosomal genome nuclear genome, the mt DNA. Most laboratories use typing based mtDNA polymorphisms in the nucleotide sequence in the noncoding region (also known as the control region, the hypervariable or D-loop) of mtDNA. However, in some haplogrupos classification may not be possible based on only control data region. Thus, studies suggest the need for additional typing single nucleotide polymorphisms (SNPs) in other regions of mtDNA, especially in cases where it is not possible to differentiate individuals only by the analysis of hypervariable region. This study aimed to analyze, analyze thirty (30) SNPs of mtDNA in samples of unrelated individuals born and living in the State of Espírito Santo, allowing their classification in haplogroups and complementing the SNPs data of mtDNA control region achieved in previous work in the laboratory, for later use in forensic cases. A total of 100 samples, 19 were found haplogroups and the sample were classified according to its origin: 43% African, 30% European, 26% Native American, and 1% Asian. The haplogroup was found more L3 having African origin. Some samples of previous work could not be correctly classified only with the sequencing of the control region of mtDNA, after analysis of 30...
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Choy, Yan-tsun. "Statistical evaluation of mixed DNA stains." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B42664287.
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Van, Winkle Carolyn. "Forensic DNA Extraction Strategies for PCR Analysis." Thesis, University of North Texas, 1998. https://digital.library.unt.edu/ark:/67531/metadc278269/.
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There is a transition nationwide on the analysis of forensic evidentiary stains containing biological material from traditional serology to Polymerase Chain Reaction (PCR) methodologies. The increased sensitivity of PCR, the limited number of alleles at each locus, and the necessity of producing unambiguous data for entry into the FBI's Combined DNA Index System make this study of extraction procedures of utmost importance. A "single tube" extraction procedure for blood stains collected onto FTA™ paper and a modified differential nonorganic extraction method from spermatozoa containing
mixed stains were analyzed and compared. The extraction success was evaluated by amplification and typing of the amplified fragment length polymorphism, D1S80. These modifications of the nonorganic method utilized gave an improved separation of the spermatozoa-containing mixed stains.
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Edlund, Hanna. "Sensitive Identification Tools in Forensic DNA Analysis." Doctoral thesis, Uppsala universitet, Institutionen för genetik och patologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-131904.
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DNA as forensic evidence is valuable in criminal investigations. Implementation of new, sensitive and fast technologies is an important part of forensic genetic research. This thesis aims to evaluate new sensitive methods to apply in forensic DNA analysis including analysis of old skeletal remains. In Paper I and II, two novel systems for analysis of STRs, based on the Pyrosequencing technology, are presented. In Paper I, Y chromosomal STRs are analysed. Markers on the male specific Y chromosome are especially useful in analysis of DNA mixtures. In Paper II, ten autosomal STRs are genotyped. The systems are based on sequencing of STR loci instead of size determination of STR fragments as in routine analysis. This provides a higher resolution since sequence variants within the repeats can be detected. Determination of alleles is based on a termination recognition base. This is the base in the template strand that is excluded from the dispensation order in the sequencing of the complementary strand and therefore terminates the reaction. Furthermore, skeletal remains are often difficult to analyse, due to damaging effects from the surrounding environment on the DNA and the high risk of exogenous contamination. Analysis of mitochondrial DNA is useful on degraded samples and in Paper III, mtDNA analysis of 700 years old skeletal remains is performed to investigate a maternal relationship. The quantity and quality of DNA are essential in forensic genetics. In Paper IV the efficiency of DNA isolation is investigated. Soaking skeletal remains in bleach is efficient for decontamination but result in a lower DNA yield, especially on pulverised skull samples. In conclusion, this thesis presents novel sequencing systems for accurate and fast analysis of STR loci that can be useful in evaluation of new loci and database assembly as well as the utility of mtDNA in forensic genetics.
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Hu, Yueqing. "Some topics in the statistical analysis of forensic DNA and genetic family data." Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/hkuto/record/B38831491.
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Wheate, Rhonda Marie Physical Environmental & Mathematical Sciences Australian Defence Force Academy UNSW. "Jury comprehension and use of forensic science." Awarded by:University of New South Wales - Australian Defence Force Academy. School of Physical, Environmental and Mathematical Sciences, 2007. http://handle.unsw.edu.au/1959.4/38644.
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The ability of jurors and juries to comprehend and utilise scientific evidence in Australian criminal trials has been examined. From mock jury surveys relating to DNA profiling evidence, it was determined that most respondents were able to comprehend some basic and applied statistics, although their ability was in part related to their knowledge of English and their level of education. The point at which mock jurors were prepared to convict an accused solely on the basis of DNA profiling evidence was examined and found to be low compared with the strength of DNA profiling evidence commonly presented in Australian courts. Mock jurors also demonstrated the ability to process evidence that was presented in a Bayesian framework; commencing with prior odds, introducing new information and culminating in posterior odds. From a survey of Australian forensic scientists, including fraud investigators, it was found that most practitioners' concerns could be addressed by greater pre-trial consultation between experts and legal advocates. Improved knowledge within the legal profession concerning the jargon, principles, procedures, limitations and conclusions to be drawn from different scientific disciplines, prior to presenting this evidence in court, is recommended as the means by which complex evidence can be better adduced from expert witnesses and better presented to juries in criminal trials. Finally, from interviewing actual jurors in criminal trials in the Australian Capital Territory it was determined that where jurors' expectations of scientific evidence, particularly DNA profiling evidence, are not met, high levels of juror frustration and speculation may culminate in hung juries. The adversarial setting of criminal proceedings was also found to produce an environment in which jurors felt that information that would assist them in reaching a verdict was being deliberately withheld. The ability of the jury to ask questions and the allowed nature of those questions were also examined, with the resultant recommendation that juries be given more explicit information at the commencement of trials to inform them about their rights and obligations when asking questions.
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Smith, Tiffany Lynn. "Investigating the potential of RNA to be used in forensic casework analysis." Morgantown, W. Va. : [West Virginia University Libraries], 2010. http://hdl.handle.net/10450/11018.
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Thesis (M.S.)--West Virginia University, 2010.Title from document title page. Document formatted into pages; contains vi, 60 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 58-60).
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Choy, Yan-tsun, and 蔡恩浚. "Statistical evaluation of mixed DNA stains." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B42664287.
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Stefaniw-Alvarez, Michelle. "Physical characteristics of an individual the identification of biomarkers for biological age determination /." Orlando, Fla. : University of Central Florida, 2007. http://purl.fcla.edu/fcla/etd/CFE0001737.
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Jackson, Carrie Beth. "A more sensitive sex determination assay." Diss., Connect to online resource - MSU authorized users, 2006.
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Derksen, Linda Anne. "Agency and structure in the history of DNA profiling : the stabilization and standardization of a new technology /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC IP addresses, 2003. http://wwwlib.umi.com/cr/ucsd/fullcit?p3083460.
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Gregonis, Daniel John. "The analysis of twelve forensic DNA genetic markers for Hardy-Weinberg and gametic phase disequilibrium for a Caucasian data base." CSUSB ScholarWorks, 1997. https://scholarworks.lib.csusb.edu/etd-project/1549.
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Jeffery, Kathryn. "Application to forensic genetics to the population biology of western lowland gorillas at LopeÌ, Gabon." Thesis, Cardiff University, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.408771.
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Counsil, Tyler I. "Real-time RNA-based amplification allows for sensitive forensic blood evidence analysis." Virtual Press, 2008. http://liblink.bsu.edu/uhtbin/catkey/1391475.
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The purpose of this experiment was to determine if nucleic acid sequence based amplification (NASBA) is a suitable application for the differentiation of body fluids that might comprise a forensic evidence sample. NASBA is a sensitive RNA transcription based amplification system. NASBA could theorhetically be used for bodily fluid identification based upon amplification of tissue-specific mRNA transcripts present in a given forensic sample.Amplification of both Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and Matrix Metalloproteinase 1 1 (MMPmRNA transcripts were used to determine that NASBA could amplify body fluid transcripts and whether it could distinguish between menstrual and non-menstrual blood, respectively. GAPDH is a housekeeping gene that is constituently expressed and its mRNA transcripts could therefore be used to determine whether non-menstrual blood could be amplified using the NASBA procedure. MMP 11 is a menstrual cycle-specific gene associated with endometrial breakdown. Using the mRNA transcripts from MMP 11, NASBA could be utilized for menstrual blood identification. In this study, non-menstrual and menstrual blood samples were analyzed with NASBA both in the presence and absence of chemical contamination. Contaminants utilized ranged from commercial automotive wax, transmission fluid, brake fluid, artificial tears, hand soap, 10% bleach, and the luminol blood detecting reagent. Non-menstrual blood was aliquoted onto a 1 cm x 1 cm cotton cloth for contamination, while menstrual blood was provided on a 1 cm x 1 cm area of sterile menstrual pad. All samples underwent Tri reagent extraction to obtain RNA samples for NASBA amplification.With respect to NASBA amplification data, non-menstrual blood data (from extracted RNA and unextracted blood samples) revealed the highest levels of amplification as shown in relative fluorescence units (RFU). Uncontaminated menstrual blood revealed the second highest amplification data. In the presence of chemical contamination, high levels of amplification were observed when samples were contaminated with brake fluid and commercial hand soap. Moderately low amplification was observed with samples contaminated with transmission fluid, 10% bleach, and artificial tears. NASBA amplification was completely inhibited in the presence of automotive wax and luminol. Cycle threshold (CO values for each amplification result were also obtained from each reaction. Smaller Ct values correspond to a higher NASBAreaction efficiency and therefore larger amplification values. The Ct values obtained for each amplified sample correlate strongly with the amount of amplification observed from reaction. Based upon the results of this experiment, NASBA should be considered as a novel tool for forensic evidence analysis.Department of Biology
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Hu, Yueqing, and 胡躍清. "Some topics in the statistical analysis of forensic DNA and genetic family data." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B38831491.
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Kemp, Philip M. (Philip Marcus). "A Forensic Marker for a Genetic Disease Often Misdiagnosed as Sudden Infant Death Syndrome (SIDS)." Thesis, University of North Texas, 1991. https://digital.library.unt.edu/ark:/67531/metadc500567/.
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Sudden Infant Death (SIDS) has been associated with medium-chain acyl-CoA dehydrogenase (MCAD) deficiency, an inborn error of fatty acid oxidation. Blood and tissue samples from a large cohort of SIDS victims were analyzed for the presence of dodecanoic acid (C₁₂) by gas chromatography. A subgroup of these cases had a significantly higher blood concentration than age-matched controls, suggesting MCAD deficiency. An animal study using Sprague-Dawley rats was done to mimic the effects of MCAD deficiency. Significantly increased blood concentrations of dodecanoic acid were observed. Decreased values in heart and liver were puzzling findings. The data indicate that dodecanoic acid is a blood marker for MCAD deficiency.
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OLIVEIRA, Tatiana Costa de. "DNA humano extraído a partir de larvas de dípteros coletadas em cadáveres no instituto médico legal de Pernambuco." Universidade Federal de Pernambuco, 2015. https://repositorio.ufpe.br/handle/123456789/17461.
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CAPEs
O uso de insetos visando responder aos quesitos levantados em investigações criminais ganhou espaço nas últimas décadas entre os pesquisadores e profissionais desta área, assim como a combinação de técnicas de genética forense para a obtenção de DNA humano a partir destes organismos, em especial dos dípteros necrófagos. Desse modo, neste estudo objetivou-se obter e testar um protocolo de identificação de DNA humano extraído a partir de larvas de dípteros coletadas em cadáveres no Instituto de Medicina Legal de Pernambuco Antonio Persivo Cunha (IMLAPC/PE). Inicialmente, espécimes imaturos foram coletados no IMLAPC/PE e criados em dieta a base de carne moída bovina para possibilitar a identificação da espécie mais abundante e frequente que se cria neste substrato. A espécie Chrysomya albiceps (Diptera: Calliphoridae) foi selecionada como modelo experimental. Grupos de larvas dessa espécie foram submetidos a uma dieta baseada em carne moída e sangue humano por 48 horas, dissecadas e submetidas a extração de DNA, utilizandose duas metodologias comumente adotadas pelos laboratórios de genética forense: Kit DNA IQ™ e Método Fenol-Clorofórmio. O DNA extraído foi quantificado através de Nanodrop® e Real-Time PCR 7500 com uso do Quantifiler® Duo DNA Quantification. Para amplificação do DNA foram usados os kits para STR (short tandem repeats): AmpFℓSTR® Identifiler® Plus PCR Kit, Argus X-12® Kit e PowerPlex® Fusion System kit. As amostras amplificadas foram analisadas por eletroforese capilar em ABI PRISM 3500, permitindo observar que, para os kits utilizados houve perfis íntegros e compatíveis com a amostra referência, a partir da extração com kit DNA IQ™ e/ou método Fenol- Clorofórmio. Além disso, foram testados quatro meios de armazenagem comumente utilizados em zoologia: etanol 70%, etanol 95%, formol 4% e via seca. Após 24 horas de armazenagem, as amostras foram submetidas aos processos de análise de DNA e o formol 4% apresentou os melhores perfis de DNA. O fato de haver perfis passíveis de comparação confirma a utilidade das larvas de dípteros usadas para este fim, as quais podem futuramente ser usadas para correlacionar perfis genéticos com uma cena criminal. O aprimoramento destas técnicas é necessário para que o uso das larvas de dípteros muscóides com emprego para a entomogenética tenha mais difusão entre os meios acadêmico e forense.
The use of insects for investigations has gained ground in recent decades among researchers and criminal professionals. Recently, the use of these animals has been combined with forensic genetics techniques for obtaining human DNA from these. Among the main focus groups for this technique are the carrion flies that have the host DNA extracted from intestinal contents. Because the visibility of this branch of forensic biology, this study aimed to obtain and test a protocol for identifying human DNA extracted from larvae of Diptera at the Instituto de Medicina Legal de Pernambuco Antonio Persivo Cunha (IMLAPC/PE). The species Chrysomya albiceps (Diptera: Calliphoridae) was selected as an experimental model. Groups of larvae of this species were subjected to diet ground meat and human blood for 48 hours, dissected and subjected to DNA extraction using two methods commonly used by forensic genetics laboratories: DNA IQ™ Kit and Method phenol-chloroform. The extracted DNA was quantified by Nanodrop® and Real-Time PCR 7500 with use of Quantifiler® Duo DNA Quantification. For DNA amplification kits for STR (short tandem repeats) were used: AmpFℓSTR® Identifiler® Plus PCR Kit, Argus X-12® Kit and PowerPlex® Fusion System kit. The amplified samples were analyzed by capillary electrophoresis in ABI PRISM 3500, allowing to observe for kits used there have upright profiles and compatible with the reference sample, from the IQ™ DNA extraction kit and/or phenol-chloroform method. In addition, four storage means commonly used in zoology were tested: 70% ethanol, 95% ethanol, 4% formaldehyde and dry. After 24 hours of storage, the samples were submitted to DNA analysis processes and the 4% formaldehyde DNA showed the best profile. The fact that there be comparable profiles confirms the usefulness of dipteran larvae used for this purpose, which can further be used to correlate genetic profiles and a criminal scene. The improvement of these techniques is required for the use of larvae dipterae with employment for the entomogenetics have more diffusion among academic and forensic means.
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Duz, Lana Maximiliano. "Evolução tecnologica dos exames de paternidade e sua validade juridica." [s.n.], 2007. http://repositorio.unicamp.br/jspui/handle/REPOSIP/290723.
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Orientador: Eduardo DarugeDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba
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Resumo: A ciência e a tecnologia vêm se sobrepujando constantemente e seus avanços repercutem nas deliberações do Poder Judiciário. Decisões sobre paternidade baseadas em técnicas, atualmente suplantadas pelo avanço da ciência, têm sido questionadas judicialmente, colocando em evidência a atividade do perito judicial. Nesse contexto, o presente trabalho de pesquisa teve por objetivo investigar de que maneira tem sido interpretada a responsabilidade do perito que emitiu laudos com resultados de exames de paternidade realizados em época anterior à utilização dos exames de DNA, para esse mesmo fim. Para o desenvolvimento deste trabalho de pesquisa foram analisados 200 exames de investigação de paternidade, realizados entre os anos de 1994 a 2001, pela técnica dos antígenos eritrocitátios e leucocitátios e 30 exames de investigação de paternidade realizados no ano de 2006, empregando-se a técnica de DNA, todos realizados na FOP-UNICAMP - Faculdade de Odontologia de Piracicaba, Departamento de Odontologia social, Área de Odontologia Legal e Deodontologia. Foram analisados, também, os aspectos jurídicos dos exames de paternidade avaliando 20 julgados ocorridos no perído entre 1991 e 2006, pelos tribunais pátrios, para verificar como tem sido vista a responsabilidade do perito pelos nossos julgadores. Toda pesquisa foi realizada na Faculdade de Odontologia de Piracicaba -UNICAMP. Atingido o seu termo, este trabalho de pesquisa científica permitiu concluir que a utilização dos exames pelos antígenos eritrocitários e até mesmo dos antígenos leucocitários, levava a um nível de credibilidade absoluta apenas quando excluíam a paternidade acusada; que os exames de DNA oferecem um índice de certeza de 99,99% em casos de investigação de paternidade, que os tribunais passaram a flexibiliar a coisa julgada material em ações nagatórias de paternidade com pedidos baseados em exames de DNA e que o perito, tendo se valido dos limites impostos pela técnica disponível em cada época, não podia ser responsabilizado pela reforma da sentença em ação negatória de paternidade, com base no exame de DNA
Abstract: The science and the technology come if constantly surpassing and its progresses rebound in the deliberations of the Judiciary Power. Decisions on paternity set in techniques, now supplanted by the progress of the science, they have been questioned judicially, placing in evidence the activity of the judicial expert. In that context, the present research work had for objective to investigate that way has been interpreted the responsibility of the expert that emitted legal issue with results of exams of paternity accomplished in time previous to the use of the exams of DNA, for that same end. For the development of this research work 200 exams of investigation of paternity were analyzed, accomplished among the years from 1994 to 2001, by the technique of the antigens eritrocitátios and leucocitátios and 30 exams of investigation of paternity accomplished in the year of 2006, being used the technique of DNA, everybody accomplished in FOP-UNICAMP - Ability of Dentistry of Piracicaba, Department of social Dentistry, Area of Legal Dentistry and Deodontology. They were analyzed, also, the juridical aspects of the exams of paternity evaluating 20 judged happened in the period between 1991 and 2006, for the tribunals of the homeland, to verify as the responsibility of the expert has been seen by our judges. Every research was accomplished in the Ability of Dentistry of Piracicaba - UNICAMP. Reached its term, this work of scientific research allowed to end that the use of the exams for the antigens eritrocitários and even of the antigens leucocitários, it just took at a level of absolute credibility when they excluded the paternity accused; that the exams of DNA offer an index of certainty of 99,99% in cases of investigation of paternity, that the tribunals passed the to move the thing judged material in actions that deny of paternity with requests based on exams of DNA and that the expert, having been worth of the limits taxes for the available technique in each time, it could not be made responsible by the reform of the sentence in action that deny of paternity, with base in the exam of DNA
Mestrado
Odontologia Legal e Deontologia
Mestre em Odontologia Legal e Deontologia
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Ambrosio, Isabela Brunelli. "Análise de SNPs do DNA mitocondrial em indivíduos residentes no estado do Espírito Santo para aplicação na Identificação Humana /." Araraquara, 2015. http://hdl.handle.net/11449/124408.
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Orientador: Regina Maria Barretto CicarelliBanca: Joyce Aparecida Martins Lopes Ferraz
Banca: Rogério Nogueira de Oliveira
Resumo: A identificação humana por meio do DNA constitui um dos produtos mais revolucionários da Genética Moderna, tornando-se uma ferramenta indispensável na investigação criminal. Essa identificação é baseada no perfil genético do indivíduo, pela combinação de diversos marcadores herdados de seus progenitores. Os marcadores são, geralmente,e diferenças nas sequências de DNA nuclear entre os indivíduos (polimorfismos). Em alguns casos, em que a análise do DNA nuclear não puder ser aplicada, a alternativa de maior sucesso é a análise do DNA mitocondrial (DNAmt). As mitocôndrias são organelas intracelulares de dupla membrana presentes em todas as células nucleadas de mamíferos, com genoma extracromossômico separado e distinto do genoma nuclear, o DNA mt. A maioria dos laboratórios que utilizam tipagem do DNAmt baseiam-se nos polimorfismos presentes na sequência de nucleotídeos na região não codificadora (também conhecida como região controle, hipervariável, ou D-loop) do DNAmt. No entanto, a classificação em alguns haplogrupos pode não ser possível com base em dados apenas da região controle. Assim, estudos sugerem a necessidade de tipagem adicional de polimorfismos de nucleotídeos únicos (SNPs) em outras regiões do DNAmt, em especial, nos casos onde não é possível diferenciar os indivíduos apenas pela análise da região hipervariável. Este trabalho teve como objetivo analisar, analisar 30 (trinta) SNPs do DNAmt em amostras de indivíduos não relacionados, nascidos e residentes no Estado do Espírito Santo, permitindo a classificação das mesmas em haplogrupos e complementando os dados de SNPs da região controle do DNAmt obtidos em trabalho anterior no laboratório, para posterior utilização em casos forense. De um total de 100 amostras, foram encontrados 19 haplogrupos e a população estudada foi classificada conforme sua origem em: 43% africana, 30% europeia...
Abstract: Human identification through DNA is one of the most revolutionary products of Modern Genetics, making it an indispensable tool in criminal investigation. This identification is based on the genetic profile of the individual, the combination of several markers inherited from their parents. The markers are generally differences in nuclear and DNA sequences between individuals (polymorphisms). In some cases, the analysis of nuclear DNA cannot be applied, the most successful alternative is the analysis of mitochondrial DNA (mtDNA). Mitochondria are intracellular organelles with a double membrane present on all nucleated mammalian cells with separate and distinct extrachromosomal genome nuclear genome, the mt DNA. Most laboratories use typing based mtDNA polymorphisms in the nucleotide sequence in the noncoding region (also known as the control region, the hypervariable or D-loop) of mtDNA. However, in some haplogrupos classification may not be possible based on only control data region. Thus, studies suggest the need for additional typing single nucleotide polymorphisms (SNPs) in other regions of mtDNA, especially in cases where it is not possible to differentiate individuals only by the analysis of hypervariable region. This study aimed to analyze, analyze thirty (30) SNPs of mtDNA in samples of unrelated individuals born and living in the State of Espírito Santo, allowing their classification in haplogroups and complementing the SNPs data of mtDNA control region achieved in previous work in the laboratory, for later use in forensic cases. A total of 100 samples, 19 were found haplogroups and the sample were classified according to its origin: 43% African, 30% European, 26% Native American, and 1% Asian. The haplogroup was found more L3 having African origin. Some samples of previous work could not be correctly classified only with the sequencing of the control region of mtDNA, after analysis of 30...
Mestre
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Barlow, Vicki. "The development of enhanced experimental strategies for the DNA analysis of low-template or compromised forensic sample types." Thesis, Northumbria University, 2015. http://nrl.northumbria.ac.uk/30231/.
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Single-cell DNA analysis is not routinely carried out in a forensic setting as it is considered unreliable due to challenges associated with DNA amplification, contamination and profile interpretation. In light of the development of increasingly sensitive techniques, the question of the reliability of single-cell DNA analysis in terms of both processing and interpretation is addressed in the first part of this thesis. Optimising all stages of the DNA analysis process has provided a sensitive method which facilitates the successful outcome of a useable profile from single-cells. Although no consensus profile can be generated for this sample type, interpretation guidelines have been set to enable the robust analysis of single cells. It has been concluded that single-cells can be reliably amplified and profiled for forensic purposes. Both DNA and textile fibres have a proven track record in forensic casework yet their analysis is rarely combined. As an application of the aforementioned single-cell DNA analysis, this project explores the possibility that when fibres are transferred from one surface to another, they could also be acting as a vector for the wearer’s own DNA, through cells that have adhered to the fibre surfaces. Fluorescent staining and microscopy is used to detect the cells in situ on the fibre surface, which are then recovered and processed for DNA using the previously optimised single-cell analysis methods, along with a newly developed DNA assay designed for the amplification of low DNA template samples. The results of this study have demonstrated that cells can be visualised in situ on the fibre surface and that there is potential for cell transfer to occur. It has been concluded however, that from a casework point of view, targeting transferred fibres for cells may not be the best approach as it is time consuming and has not been shown to be effective in this study. The final part of this thesis is focused on the efficacy of massively parallel sequencing (MPS) technology for samples that are expected to be severely degraded due to age or exposure to a hostile environment. The ability of both the recently launched Illumina ForenSeq™ DNA Signature Prep Kit for nuclear DNA markers and an in-house method for the sequencing of degraded mitochondrial DNA, have been tested to determine if MPS offers a more comprehensive evaluation of degraded material than the traditional PCR-CE methods. The results of the ForenSeq kit have demonstrated the effectiveness of its low molecular weight STR and SNP markers for amplifying low template, degraded DNA samples, with alleles amplified using less than 20 pg total DNA input. This kit has also therefore shown application in the field of bioarchaeology, as it can provide the biological sex of the sample, biogeographic ancestry information and also aids detection of sample/control contamination. The in-house mitochondrial DNA assay resulted in the successful amplification and sequencing of samples for which no nuclear DNA was amplified. The high depth of read coverage in these samples, average of 18,000, allowed for the identification of even low level variants.
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Graversen, Therese. "Statistical and computational methodology for the analysis of forensic DNA mixtures with artefacts." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:4c3bfc88-25e7-4c5b-968f-10a35f5b82b0.
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This thesis proposes and discusses a statistical model for interpreting forensic DNA mixtures. We develop methods for estimation of model parameters and assessing the uncertainty of the estimated quantities. Further, we discuss how to interpret the mixture in terms of predicting the set of contributors. We emphasise the importance of challenging any interpretation of a particular mixture, and for this purpose we develop a set of diagnostic tools that can be used in assessing the adequacy of the model to the data at hand as well as in a systematic validation of the model on experimental data. An important feature of this work is that all methodology is developed entirely within the framework of the adopted model, ensuring a transparent and consistent analysis. To overcome the challenge that lies in handling the large state space for DNA profiles, we propose a representation of a genotype that exhibits a Markov structure. Further, we develop methods for efficient and exact computation in a Bayesian network. An implementation of the model and methodology is available through the R package DNAmixtures.
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Ara, Andleeb. "Development of NASBA-primer search software for designing forensic saliva tandem repeat markers for mucin and amylase." Muncie, Ind. : Ball State University, 2009. http://cardinalscholar.bsu.edu/635.
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Valenzuela, Robert Keams. "Predictive Modeling for Complex Traits: Normal Human Pigmentation Variation." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/145309.
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Melanin pigmentation is a complex trait governed by many genes. Variation in melanin pigmentation within, and between, populations makes it an important trait for assisting in physical identification of an individual in forensic investigations. Utilizing a training sample (n=789) comprised of various ethnicities and SNPs (75) in 24 genes previously implicated in human or animal pigmentation studies, I determined three-SNP multiple linear regression models that accounted for large proportions of pigmentation variation in skin (45.7%), eye color (76.4%), and hair [eumelanin-to-pheomelanin (43.2%) and total melanin (76.3%)], independent of ethnic origin. Rather than implementing stepwise regression, to ascertain the three-SNP predictive models, I devised an algorithm that is likely more robust than stepwise regression. The algorithm consisted of two steps: the first step reduced the pool of 75 SNPs to a pool of 40 by selection of SNPs that were significant (p<0.05) by one-way ANOVA; the second step enabled selection of SNPs for model incorporation based on their frequency in the best-fitted models of all possible combinations of three-SNP models (i.e., 40 choose 3).Prediction models were validated utilizing an independent cohort (n=242, test sample) that was very similar in ethnic composition to the training sample. Relative shrinkage was moderate for skin reflectance (23.4%), eye color (19.4%), and eumelanin-to-pheomelanin (37.3%) of hair, and largest for total melanin (67%) of hair. Additionally, we refined our model-building algorithm, enabling visual comparison of the frequency and co-linearity due to linkage or co-inheritance of SNPs of the best-fitted models. Application of our algorithm to the test sample yielded the same or similar models as the training sample. Two of the three SNPs composing the models were the same, with some variability in the third SNP of the model.
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Schlaphoff, Theresa Elizabeth-Anne. "A study to evaluate variable number of tandem repeat DNA polymorphisms in disputed paternity testing." Thesis, Cape Technikon, 1993. http://hdl.handle.net/20.500.11838/1465.
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Thesis (MDip (Medical Technology))--Cape Technikon, 1993The use of genetic marker testing to resolve cases of disputed paternity, is well established. The number and range of systems used depends on the expertise of the laboratory, and for this reason various laboratories offer different systems. Standard testing includes tests in the following genetic marker systems: human leukocyte antigen (tissue) typing; red cell blood groups; and red cell enzyme and serum protein testing. The Provincial Laboratory for Tissue Immunology currently offers a range of 16 genetic marker systems capable of excluding >99% of falsely accused men. Following the discovery DNA polymorphisms, particularly VNTR DNA polymorphisms, and the commercial availability of VNTR DNA probes, PLTI decided to offer this service to our clients. This study was the initial phase in the establishment of a VNTR DNA typing laboratory and covered the determination of inter-and intra-gel accuracy and precision, selection of restriction enzyme/probe combination, and evaluation and comparison of the results of 100 disputed paternity cases tested using both standard and VNTR DNA typing. Of the 100 cases tested, in 33 cases, the putative father was excluded using standard testing. These exclusions were confirmed using VNTR DNA typing, and, furthermore, an additional two exclusions of paternity were shown using only VNTR DNA typing. In another two cases of disputed paternity, the exclusions obtained using standard tests required further confirmation. VNTR DNA typing convincingly excluded both falsely accused putative fathers. The VNTR DNA typing laboratory now functions as an integral part of the disputed paternity service. Due to the cost and time involved in VNTR DNA typing it is reserved at this stage for: those cases which require further confirmation of the results of standard testing; when the probability of paternity is low (<99.7%); or when a specific request is made.
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Chung, Denise T. "The development of novel STR miniplex primer sets for the analysis of degraded and compromised DNA samples." Ohio : Ohio University, 2004. http://www.ohiolink.edu/etd/view.cgi?ohiou1097609199.
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Jacobs, Gwynneth. "Evaluation of insertion-deletion polymorphisms with the kit Qiagen Investigator® DIPplex for forensic application in South Africa." University of the Western Cape, 2015. http://hdl.handle.net/11394/4690.
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>Magister Scientiae - MScInsertion-deletion polymorphisms (indels) have been underutilized in forensic identification of individuals in comparison with single nucleotide polymorphisms (SNPs) and short tandem repeat (STRs) systems. The use of indels for the purpose of human identification is more advantageous than previously used methods as it combines desirable characteristics of both the SNPs and STRs i.e. low costs and simplistic typing methods as well as indels having small amplicons size, making them suitable for genotyping highly degraded DNA. Currently there is only one commercial kit available for the forensic community, the Investigator® DIPlex kit (Qiagen), which cover a total of 30 indel loci distributed over 19 autosomal chromosomes. The objective of this study was to evaluate the Qiagen Investigator® DIPplex kit for forensic application in South Africa. The kit‘s performance was evaluated by comparing different extraction methods; sensitivity, robustness and reproducibility were evaluated and forensic parameters (match probability, power of discrimination, polymorphism information content, power of exclusion and typical paternity index) were estimated based on population data generated from five South African populations (Afrikaner, Mixed Ancestry, Indian-Asian, Xhosa and Zulu). Population comparisons were performed using Fst-analysis, factorial component analysis as well as phylogenetic tree construction. DNA was extracted from buccal swabs and whole blood collected from a total of 512 individuals from the five South African population groups and genotyped using the Qiagen Investigator® DIPplex kit. Sanger DNA sequencing and sequence alignments confirmed the presence of a null allele at locus HLD97 which was present in high frequency in the Xhosa and Zulu populations. This observation was made in 14 individuals belonging to the Xhosa and Zulu populations. Null allele frequencies in all five South African populations were also estimated. Null alleles were estimated for all loci using analytical methods i.e. Charkraborty null allele estimator, Brookfield null allele estimators 1 and 2 and ML-NullFreq software program. The kit performed well in the laboratory, not requiring any additional reagents or instrumentation and successfully generating profiles with input DNA amounts as low as 0.2 ng/μL. Although well suited for forensic application, the Qiagen Investigator® DIPplex kit showed some drawbacks with regards to application on South African populations. The presence of a null allele at the HLD97 locus as well as indication of population substructure affects allele frequency estimates for the South African populations. Correction for population substructure as present within the South African populations should be considered using FST analysis and it is recommended that the HLD97 locus should be excluded from any kinship analysis performed on South African populations.
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Warren, Joseph E. "Mutation Rate Analysis of the Human Mitochondrial D-loop and its Implications for Forensic Identity Testing." Thesis, University of North Texas, 2000. https://digital.library.unt.edu/ark:/67531/metadc2492/.
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To further facilitate mitochondrial DNA (mtDNA) sequence analysis for human identity testing, a better understanding of its mutation rate is needed. Prior to the middle 1990's the mutation rate applied to a forensic or evolutionary analysis was determined by phylogenetic means, This method involved calculating genetic distances as determined by amino acid or DNA sequence variability within or between species. The mutation rate as determined by this method ranged from 0.025-0.26 nucleotide substitutions/ site/ myr (million years). With the recent advent of mtDNA analysis as a tool in human identity testing an increased number of observations have recently come to light calling into question the mutation rate derived from the phylogenetic method. The mutation rate as observed from forensic analysis appears to be much higher than that calculated phylogenetically. This is an area that needs to be resolved in human identity testing. Mutations that occur within a maternal lineage can lead to a possible false exclusion of an individual as belonging to that lineage. A greater understanding of the actual rate of mutation within a given maternal lineage can assist in determining criteria for including or excluding individuals as belonging to that lineage. The method used to assess the mutation rate in this study was to compare mtDNA sequences derived from the HVI and HVII regions of the D-loop from several different maternal lineages. The sequence information was derived from five unrelated families consisting of thirty-five individuals. One intergenerational mutational event was found. This derives to approximately 1.9 nucleotide substitutions/ site/ myr. This mutation rate was very consistent with several other similar studies. This increased mutation rate needs to be considered by forensic testing laboratories performing mtDNA sequence analysis prior to formulating any conclusive results.
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Ehrenreich, Liezle Suzette. "The evaluation of Y-STR loci for use in forensics." Thesis, University of the Western Cape, 2005. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_9766_1228396041.
Full textAbstract:
The aim of this study was to investigate the forensic usefulness of various Y-chromosome short tandem repeat loci among South African sub-populations. Three different sets of Y-chromosome short tandem repeat loci were chosen for investigation.
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Groß, Theresa Elisa [Verfasser]. "Development of novel SNP panels for the application of massively parallel sequencing to forensic genetics / Theresa Elisa Groß." Köln : Deutsche Zentralbibliothek für Medizin, 2017. http://d-nb.info/1144184878/34.
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Candido, Ian Marques. "COMPARAÇÃO ENTRE AS TÉCNICAS DE EXTRAÇÃO DE DNA EM OSSO HUMANO POR PARTÍCULAS MAGNÉTICAS E COLUNA DE SÍLICA." Pontifícia Universidade Católica de Goiás, 2013. http://localhost:8080/tede/handle/tede/2359.
Full textAbstract:
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Previous issue date: 2013-02-08The identification of human remains in decomposition, charred, skeletal remains and mass disasters can be performed by Forensic Genetics and, in most cases, bones and teeth are the only viable source for DNA typing .Thus, considering the large number of bones used in human identification and the need for standardization of DNA extraction in this kind of sample, the aim of this study is to compare two techniques of DNA extraction, with the possibility of automation. The analysis was performed on twenty five human bones evaluating the quantity of the extracted genetic material, genetic profiles obtained for each sample and the time analysis by method used. With magnetic bead in platform automated, analysis time was 3 hours to process 12 samples, whereas by silica column four samples in 27 hours. Magnetic bead recovered a larger amount of DNA in 88% of samples. 68% of the samples magnetic particle had a high amplification partial (9/16 loci) and silica column only 36%. Therefore, the method used magnetic bead is suitable for automating the extraction processes.
A identificação humana de restos mortais em avançado estado de decomposição, carbonizados, desastres em massa e esqueletizados pode ser realizada pela Genética Forense e, na maioria das vezes, ossos e dentes são as únicas fontes de DNA viáveis para análise. Dessa maneira, considerando o grande número de ossos utilizados na identificação humana e a necessidade de padronização da técnica de extração de DNA nesse tipo de amostra, o objetivo do presente trabalho é comparar duas técnicas de extração de DNA, com possibilidade de automação. A análise foi realizada em vinte e cinco ossos humanos avaliando a quantidade do material genético extraído, os perfis genéticos obtidos em cada amostra e o tempo de análise gasto pela metodologia de extração. Com a metodologia de extração por partículas magnéticas utilizando plataforma automatizada, o tempo de análise foi de 3 horas para processar 12 amostras, enquanto que por coluna de sílica 4 amostras em 27 horas. Partícula magnética recuperou uma maior quantidade de DNA em 88% das amostras. 68% das amostras extraídas por partículas magnéticas tiveram uma amplificação parcial alta (9/16 loci) e por coluna de sílica apenas 36%. Por conseguinte, a metodologia de extração por partículas magnéticas é apropriada para a automatização dos processos de extração.
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Wagner, Sarah Jean. "Efficiency of DNA Recovery from Different Swab Types by qPCR." Bowling Green State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1616962034143618.
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SIMÔES, DUTRA CORREA HEITOR. "ASSESSING THE USEFULNESS OF RAMAN SPECTROSCOPY AND LIPID ANALYSIS OF DECOMPOSED HUMAN BONES IN FORENSIC GENETICS AND MOLECULAR TAPHONOMY STUDIES." Doctoral thesis, Università degli studi di Brescia, 2022. http://hdl.handle.net/11379/559020.
Full textAbstract:
Forensic DNA testing is the application of genetic analyses to help elucidate legal disputes. DNA analyses can be performed not only on biological samples from living persons, but also from deceased individuals or their decomposed remains. Such analyses have been extremely valuable to society, allowing the formal identification of countless missing persons and unidentified human remains. In practice, mineralized organs, such as bones, are among the structures most likely to be recovered after death. Decomposition is a complex process that leads to transformation and degradation of all molecules, including DNA. However, the physicochemical properties that give bones their post-mortem resilience become major obstacles when DNA is to be extracted for analysis. Thus, genetic analysis on bones is laborious and technically challenging. Physicochemical techniques, such as vibrational spectroscopy, have the potential to be used as a screening tool for DNA analysis from bones. Other molecular techniques, such as gas chromatography coupled with mass spectrometry (GC/MS) may also help to shed light onto the decomposition process and improve efficiency of DNA analysis. The objective of this research was to conduct alternative molecular investigations on decomposed bones to assess their utility in basic research and forensic casework. Femur samples collected from 50 human bodies found in an advanced state of decomposition were studied. Raman spectroscopy was conducted on thin femur slices and GC/MS was carried out on lipids extracted from powdered samples. Assessment of nuclear DNA quantity, quality, and short tandem repeat (STR) genotyping efficiency from femur fragments was also performed. Raman parameters (crystallinity, carbonate to phosphate ratio, mineral to matrix ratio) and lipids detected by GC/MS were recorded. Six types of fatty acid methyl esters (FAMEs) as well as some hydrocarbons were detected in the bone samples. The main phosphate peak position in Raman spectra was shown to be significantly correlated with preserved DNA (p=0.03713). However, remaining Raman parameters and lipids detected were not significantly correlated with DNA presence nor STR typing efficiency. Even though high background fluorescence posed a challenge in Raman spectroscopy, hampering analysis of 18% (9 of 50) of the femurs studied, it may be a useful screening tool in forensic genetics. The detection of FAMEs in the bone matrix suggests a reaction between methanol produced by bacteria and free fatty acids, which does not seem to impact the level of preservation of endogenous DNA. Overall, the molecular techniques studied have showed that the prediction of genotyping success is challenging even in short PMIs, such as in forensic contexts.Il test del DNA forense è l'applicazione di analisi genetiche per aiutare a chiarire le controversie legali. Le analisi del DNA possono essere eseguite non solo su campioni biologici di persone viventi, ma anche su individui deceduti o sui loro resti decomposti. Tali analisi sono state estremamente preziose per la società, consentendo l'identificazione formale di innumerevoli persone scomparse e resti umani non identificati. In pratica, gli organi mineralizzati, come le ossa, sono tra le strutture con maggiori probabilità di essere recuperate dopo la morte. La decomposizione è un processo complesso che porta alla trasformazione e alla degradazione di tutte le molecole, compreso il DNA. Tuttavia, le proprietà fisico-chimiche che conferiscono alle ossa la loro resilienza post mortem diventano i principali ostacoli quando il DNA deve essere estratto per l'analisi. Pertanto, l'analisi genetica sulle ossa è laboriosa e tecnicamente impegnativa. Le tecniche fisico-chimiche, come la spettroscopia vibrazionale, hanno il potenziale per essere utilizzate come strumento di screening per l'analisi del DNA dalle ossa. Altre tecniche molecolari, come la gascromatografia accoppiata alla spettrometria di massa (GC/MS), possono anche aiutare a fare luce sul processo di decomposizione e migliorare l'efficienza dell'analisi del DNA. L'obiettivo di questa ricerca era di condurre indagini molecolari alternative sulle ossa decomposte per valutarne l'utilità nella ricerca di base e nella casistica forense. Sono stati studiati campioni di femore raccolti da 50 corpi umani trovati in uno stato avanzato di decomposizione. La spettroscopia Raman è stata condotta su fette sottili di femore e la GC/MS è stata eseguita su lipidi estratti da campioni in polvere. È stata inoltre eseguita la valutazione della quantità, della qualità e dell'efficienza della genotipizzazione della ripetizione in tandem breve (STR) del DNA nucleare dai frammenti del femore. Sono stati registrati i parametri Raman (cristallinità, rapporto carbonato/fosfato, rapporto minerale/matrice) e lipidi rilevati mediante GC/MS. Nei campioni ossei sono stati rilevati sei tipi di esteri metilici degli acidi grassi (FAME) e alcuni idrocarburi. È stato dimostrato che la posizione del picco principale del fosfato negli spettri Raman è significativamente correlata al DNA conservato (p = 0,03713). Tuttavia, i restanti parametri Raman e lipidi rilevati non erano significativamente correlati alla presenza del DNA né all'efficienza della tipizzazione STR. Anche se l'elevata fluorescenza di fondo ha rappresentato una sfida nella spettroscopia Raman, ostacolando l'analisi del 18% (9 su 50) dei femori studiati, può essere un utile strumento di screening nella genetica forense. Il rilevamento di FAME nella matrice ossea suggerisce una reazione tra il metanolo prodotto dai batteri e gli acidi grassi liberi, che non sembra influenzare il livello di conservazione del DNA endogeno. Nel complesso, le tecniche molecolari studiate hanno dimostrato che la previsione del successo della genotipizzazione è impegnativa anche in PMI brevi, come in contesti forensi.
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SIMÔES, DUTRA CORREA HEITOR. "ASSESSING THE USEFULNESS OF RAMAN SPECTROSCOPY AND LIPID ANALYSIS OF DECOMPOSED HUMAN BONES IN FORENSIC GENETICS AND MOLECULAR TAPHONOMY STUDIES." Doctoral thesis, Università degli studi di Brescia, 2022. http://hdl.handle.net/11379/559017.
Full textAbstract:
Forensic DNA testing is the application of genetic analyses to help elucidate legal disputes. DNA analyses can be performed not only on biological samples from living persons, but also from deceased individuals or their decomposed remains. Such analyses have been extremely valuable to society, allowing the formal identification of countless missing persons and unidentified human remains. In practice, mineralized organs, such as bones, are among the structures most likely to be recovered after death. Decomposition is a complex process that leads to transformation and degradation of all molecules, including DNA. However, the physicochemical properties that give bones their post-mortem resilience become major obstacles when DNA is to be extracted for analysis. Thus, genetic analysis on bones is laborious and technically challenging. Physicochemical techniques, such as vibrational spectroscopy, have the potential to be used as a screening tool for DNA analysis from bones. Other molecular techniques, such as gas chromatography coupled with mass spectrometry (GC/MS) may also help to shed light onto the decomposition process and improve efficiency of DNA analysis. The objective of this research was to conduct alternative molecular investigations on decomposed bones to assess their utility in basic research and forensic casework. Femur samples collected from 50 human bodies found in an advanced state of decomposition were studied. Raman spectroscopy was conducted on thin femur slices and GC/MS was carried out on lipids extracted from powdered samples. Assessment of nuclear DNA quantity, quality, and short tandem repeat (STR) genotyping efficiency from femur fragments was also performed. Raman parameters (crystallinity, carbonate to phosphate ratio, mineral to matrix ratio) and lipids detected by GC/MS were recorded. Six types of fatty acid methyl esters (FAMEs) as well as some hydrocarbons were detected in the bone samples. The main phosphate peak position in Raman spectra was shown to be significantly correlated with preserved DNA (p=0.03713). However, remaining Raman parameters and lipids detected were not significantly correlated with DNA presence nor STR typing efficiency. Even though high background fluorescence posed a challenge in Raman spectroscopy, hampering analysis of 18% (9 of 50) of the femurs studied, it may be a useful screening tool in forensic genetics. The detection of FAMEs in the bone matrix suggests a reaction between methanol produced by bacteria and free fatty acids, which does not seem to impact the level of preservation of endogenous DNA. Overall, the molecular techniques studied have showed that the prediction of genotyping success is challenging even in short PMIs, such as in forensic contexts.Il test del DNA forense è l'applicazione di analisi genetiche per aiutare a chiarire le controversie legali. Le analisi del DNA possono essere eseguite non solo su campioni biologici di persone viventi, ma anche su individui deceduti o sui loro resti decomposti. Tali analisi sono state estremamente preziose per la società, consentendo l'identificazione formale di innumerevoli persone scomparse e resti umani non identificati. In pratica, gli organi mineralizzati, come le ossa, sono tra le strutture con maggiori probabilità di essere recuperate dopo la morte. La decomposizione è un processo complesso che porta alla trasformazione e alla degradazione di tutte le molecole, compreso il DNA. Tuttavia, le proprietà fisico-chimiche che conferiscono alle ossa la loro resilienza post mortem diventano i principali ostacoli quando il DNA deve essere estratto per l'analisi. Pertanto, l'analisi genetica sulle ossa è laboriosa e tecnicamente impegnativa. Le tecniche fisico-chimiche, come la spettroscopia vibrazionale, hanno il potenziale per essere utilizzate come strumento di screening per l'analisi del DNA dalle ossa. Altre tecniche molecolari, come la gascromatografia accoppiata alla spettrometria di massa (GC/MS), possono anche aiutare a fare luce sul processo di decomposizione e migliorare l'efficienza dell'analisi del DNA. L'obiettivo di questa ricerca era di condurre indagini molecolari alternative sulle ossa decomposte per valutarne l'utilità nella ricerca di base e nella casistica forense. Sono stati studiati campioni di femore raccolti da 50 corpi umani trovati in uno stato avanzato di decomposizione. La spettroscopia Raman è stata condotta su fette sottili di femore e la GC/MS è stata eseguita su lipidi estratti da campioni in polvere. È stata inoltre eseguita la valutazione della quantità, della qualità e dell'efficienza della genotipizzazione della ripetizione in tandem breve (STR) del DNA nucleare dai frammenti del femore. Sono stati registrati i parametri Raman (cristallinità, rapporto carbonato/fosfato, rapporto minerale/matrice) e lipidi rilevati mediante GC/MS. Nei campioni ossei sono stati rilevati sei tipi di esteri metilici degli acidi grassi (FAME) e alcuni idrocarburi. È stato dimostrato che la posizione del picco principale del fosfato negli spettri Raman è significativamente correlata al DNA conservato (p = 0,03713). Tuttavia, i restanti parametri Raman e lipidi rilevati non erano significativamente correlati alla presenza del DNA né all'efficienza della tipizzazione STR. Anche se l'elevata fluorescenza di fondo ha rappresentato una sfida nella spettroscopia Raman, ostacolando l'analisi del 18% (9 su 50) dei femori studiati, può essere un utile strumento di screening nella genetica forense. Il rilevamento di FAME nella matrice ossea suggerisce una reazione tra il metanolo prodotto dai batteri e gli acidi grassi liberi, che non sembra influenzare il livello di conservazione del DNA endogeno. Nel complesso, le tecniche molecolari studiate hanno dimostrato che la previsione del successo della genotipizzazione è impegnativa anche in PMI brevi, come in contesti forensi.
45
SIMÔES, DUTRA CORREA HEITOR. "ASSESSING THE USEFULNESS OF RAMAN SPECTROSCOPY AND LIPID ANALYSIS OF DECOMPOSED HUMAN BONES IN FORENSIC GENETICS AND MOLECULAR TAPHONOMY STUDIES." Doctoral thesis, Università degli studi di Brescia, 2022. http://hdl.handle.net/11379/559015.
Full textAbstract:
Forensic DNA testing is the application of genetic analyses to help elucidate legal disputes. DNA analyses can be performed not only on biological samples from living persons, but also from deceased individuals or their decomposed remains. Such analyses have been extremely valuable to society, allowing the formal identification of countless missing persons and unidentified human remains. In practice, mineralized organs, such as bones, are among the structures most likely to be recovered after death. Decomposition is a complex process that leads to transformation and degradation of all molecules, including DNA. However, the physicochemical properties that give bones their post-mortem resilience become major obstacles when DNA is to be extracted for analysis. Thus, genetic analysis on bones is laborious and technically challenging. Physicochemical techniques, such as vibrational spectroscopy, have the potential to be used as a screening tool for DNA analysis from bones. Other molecular techniques, such as gas chromatography coupled with mass spectrometry (GC/MS) may also help to shed light onto the decomposition process and improve efficiency of DNA analysis. The objective of this research was to conduct alternative molecular investigations on decomposed bones to assess their utility in basic research and forensic casework. Femur samples collected from 50 human bodies found in an advanced state of decomposition were studied. Raman spectroscopy was conducted on thin femur slices and GC/MS was carried out on lipids extracted from powdered samples. Assessment of nuclear DNA quantity, quality, and short tandem repeat (STR) genotyping efficiency from femur fragments was also performed. Raman parameters (crystallinity, carbonate to phosphate ratio, mineral to matrix ratio) and lipids detected by GC/MS were recorded. Six types of fatty acid methyl esters (FAMEs) as well as some hydrocarbons were detected in the bone samples. The main phosphate peak position in Raman spectra was shown to be significantly correlated with preserved DNA (p=0.03713). However, remaining Raman parameters and lipids detected were not significantly correlated with DNA presence nor STR typing efficiency. Even though high background fluorescence posed a challenge in Raman spectroscopy, hampering analysis of 18% (9 of 50) of the femurs studied, it may be a useful screening tool in forensic genetics. The detection of FAMEs in the bone matrix suggests a reaction between methanol produced by bacteria and free fatty acids, which does not seem to impact the level of preservation of endogenous DNA. Overall, the molecular techniques studied have showed that the prediction of genotyping success is challenging even in short PMIs, such as in forensic contexts.Il test del DNA forense è l'applicazione di analisi genetiche per aiutare a chiarire le controversie legali. Le analisi del DNA possono essere eseguite non solo su campioni biologici di persone viventi, ma anche su individui deceduti o sui loro resti decomposti. Tali analisi sono state estremamente preziose per la società, consentendo l'identificazione formale di innumerevoli persone scomparse e resti umani non identificati. In pratica, gli organi mineralizzati, come le ossa, sono tra le strutture con maggiori probabilità di essere recuperate dopo la morte. La decomposizione è un processo complesso che porta alla trasformazione e alla degradazione di tutte le molecole, compreso il DNA. Tuttavia, le proprietà fisico-chimiche che conferiscono alle ossa la loro resilienza post mortem diventano i principali ostacoli quando il DNA deve essere estratto per l'analisi. Pertanto, l'analisi genetica sulle ossa è laboriosa e tecnicamente impegnativa. Le tecniche fisico-chimiche, come la spettroscopia vibrazionale, hanno il potenziale per essere utilizzate come strumento di screening per l'analisi del DNA dalle ossa. Altre tecniche molecolari, come la gascromatografia accoppiata alla spettrometria di massa (GC/MS), possono anche aiutare a fare luce sul processo di decomposizione e migliorare l'efficienza dell'analisi del DNA. L'obiettivo di questa ricerca era di condurre indagini molecolari alternative sulle ossa decomposte per valutarne l'utilità nella ricerca di base e nella casistica forense. Sono stati studiati campioni di femore raccolti da 50 corpi umani trovati in uno stato avanzato di decomposizione. La spettroscopia Raman è stata condotta su fette sottili di femore e la GC/MS è stata eseguita su lipidi estratti da campioni in polvere. È stata inoltre eseguita la valutazione della quantità, della qualità e dell'efficienza della genotipizzazione della ripetizione in tandem breve (STR) del DNA nucleare dai frammenti del femore. Sono stati registrati i parametri Raman (cristallinità, rapporto carbonato/fosfato, rapporto minerale/matrice) e lipidi rilevati mediante GC/MS. Nei campioni ossei sono stati rilevati sei tipi di esteri metilici degli acidi grassi (FAME) e alcuni idrocarburi. È stato dimostrato che la posizione del picco principale del fosfato negli spettri Raman è significativamente correlata al DNA conservato (p = 0,03713). Tuttavia, i restanti parametri Raman e lipidi rilevati non erano significativamente correlati alla presenza del DNA né all'efficienza della tipizzazione STR. Anche se l'elevata fluorescenza di fondo ha rappresentato una sfida nella spettroscopia Raman, ostacolando l'analisi del 18% (9 su 50) dei femori studiati, può essere un utile strumento di screening nella genetica forense. Il rilevamento di FAME nella matrice ossea suggerisce una reazione tra il metanolo prodotto dai batteri e gli acidi grassi liberi, che non sembra influenzare il livello di conservazione del DNA endogeno. Nel complesso, le tecniche molecolari studiate hanno dimostrato che la previsione del successo della genotipizzazione è impegnativa anche in PMI brevi, come in contesti forensi.
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Khoory, Haifa. "The feasibility of transferring cells from archived buccal swabs to FTA card for long term and simple storage of forensic samples." University of Western Australia. Centre for Forensic Science, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0088.
Full textAbstract:
[Truncated abstract] The collection of buccal cells is common practise in the epidemiological and forensic science. Unlike venipuncture collection of blood; it is a safer, non-invasive method for collection of biological material. The methods by which these cells are collected from the inner cheek of an individual and stored are the key elements in preserving DNA. Typically, forensic samples require long term storage. Samples are commonly collected on cotton swabs and stored moist at low to ultra-low temperatures (less than -20oC). Although this is the method of choice in most forensic facilities, there are drawbacks. The samples are inherently contaminated with microflora within the oral cavity and the moisture allows a plethora of microorganisms to grow. As the time frame that has elapsed from collection to storage increases, there is an exponential increase in bacterial cells. Storage of containers containing swabs coated with cells at temperatures below 20oC is also costly due to requirements for large freezers which are running and monitored over 24 hours. In the pass 10 to 15 years, researchers have focussed on alternative ways to store buccal cells. The FTA card system by Whatman is one such development. The FTA card is unique in that it provides a means for the collection of buccal cells for storage at room temperature. DNA profiling from samples stored in this way for 11 years has been successfully achieved. The filter paper matrix of the FTA card binds and subsequently lyses cells. ... (2) The second component of this thesis describes a study which subjected cells on buccal swabs to various conditions of increased temperature over periods of time to establish if DNA could be amplified. The aim was to mimic exposure to the vigours of field conditions, particularly in the extreme local environments that prevail in the United Arab Emirates. a. Initially, buccal cells stored at -20oC over 360 days were used to mimic standard archiving procedures. The cells were subsequently transferred to FTA cards, amplified and profiled by using ABI AmpFLSTR Identifiler PCR Amplification Kit (Applied Biosystems, Foster City, CA). Complete STR profiles were successfully recovered from the archived swabs. In most cases 100% of alleles were recovered, suggesting that it is feasible to transfer DNA from properly archived buccal swabs to FTA cards. b. The second phase involved the storage of fresh swabs that had been artificially aged by using incubation temperatures ranging from 40oC to 100oC. Partial profiles resulted from artificially aged samples, indicating that the prevailing conditions prior to low temperature storage of the swabs plays an important role in ensuring cellular integrity and thus, DNA quality. Results from this study suggest that it is possible for biological samples stored under correct conditions to be transferred from swabs to FTA card. In combination, the two chapters presented in this study show that it is feasible to transfer achieved forensic biology samples from swabs to the FTA card system. However, it is necessary to ensure that the samples are treated in the correct manner so as to minimise contamination from external sources and to maintain the correct environmental state to maintain intact cells and usable DNA.
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Pitt, Alison Patricia. "Comparison of Middle Eastern Bedouin genotypes with previously studies populations using polymorphic Alu insertions." University of Western Australia. Centre for Forensic Science, 2009. http://theses.library.uwa.edu.au/adt-WU2009.0119.
Full textAbstract:
[Truncated abstract] Polymorphic Alu insertions (POALINs) are known to contribute to the variation and genetic diversity of the human genome. In this report specific POALINs of the Major Histocompatibility Complex (MHC) were studied. Previous population studies on the MHC POALINs have focused on individuals of African, European and Asian descent. In this study, we expand the research by studying a new and previously uncharacterised population, focusing on the Bedouin from the Middle East. Specifically we report on the individual insertion frequencies of four POALINs within the MHC class I region of this population. POALINs are members of a young Alu subfamily that have only recently been inserted into the human genome. POALINs are either present or absent at particular sites. Individuals that share the inserted (or deleted) polymorphism inherited the insertion (or deletion) from a common ancestor, making Alu alleles identical by decent. In population genetics a comparison of the resulting products from each population can then be done by comparing the lengths of the PCR products in a series of unrelated individuals and may also detect polymorphisms with regard to the presence or absence of the Alu repeats. As a direct result of their abundance and sequence identity, they promote genetic recombination events that are responsible for large-scale deletions, duplication and translocations. The deletions occur mostly in the A-T rich regions and have found to be unlikely to have been created independently of the insertions of the Alu elements (Callinan et al, 2005) The easy genotyping of the POALINs has proven to be very valuable as lineage markers for the study of human population genetics, pedigree and forensics as well as genomic diversity and evolution. POALINs have been used in a range of applications, primarily focusing on anthropological analysis of human populations. As a result of its ease of use and its utility as a marker in human evolutions studies, combining the POALINs along with other markers used in forensics could lead to improved identity testing in forensic science. More specifically, in combination with more traditional markers, race specific genotypes and haplotypes could be used for profiling crime scene samples. ... This is supported by previously reported molecular data using various types of genetic markers. In a study using six separate Alu genes, Antunez-de-Mayolo et al were able to generate a phylogenetic tree, in which the biogeographical groups followed a pattern. The biogeographical groups started with African populations that were found to relate closely to the hypothetical ancestral African population. The African populations were then followed in order by Southwest Asian populations, European populations which include Middle Eastern groups (Antunez-de-Mayolo et al, 2002). This study shows the similarities and differences between the frequencies of the Middle Eastern Bedouin and the rest of the compared populations. Though no clear results were determined, the information from the POALINs along with information provided from other genetic markers can lead to further research on the Bedouin population and the improvement of the forensic population database in order to accurately test individual ethnic background of samples to be analysed.
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Sánchez-Molero, Núñez Olallo-Efrén. "Muerte súbita natural inexplicada: valor de la investigación genética post mortem." Doctoral thesis, Universitat de Girona, 2017. http://hdl.handle.net/10803/666973.
Full textAbstract:
Natural death defines the death primarily attributed to an illness or an internal malfunction of the body, and not directly influenced by external forces. Most causes can be identified directly with macroscopic forensic analysis. However, when a macroscopic cause is not evident, the final identification of causality can become tedious and complicated. This study therefore demonstrates that identification of such genetic alterations may help to identify the etiology and also the underlying cause in such deaths Finally identification of genetic variations enables genetic counselling and undertaking of preventive measures in relatives at riskLa muerte natural define la muerte principalmente atribuida a una enfermedad o a un malfuncionamiento interno corporal, y que no está influenciada directamente por fuerzas o agentes externos. La mayoría de las causas se pueden identificar directamente con el análisis forense macroscópico. No obstante cuando la causa macroscópica no es evidente, la identificación final de la causa puede llegar a ser laboriosa y complicada. El estudio demuestra por lo tanto que la identificación de este tipo de alteraciones genéticas puede ayudar a identificar la etiología y por lo tanto la causa subyacente en este tipo de muertes. Finalmente la identificación de variantes genéticas en la autopsia molecular pone en relevancia la importancia del asesoramiento genético y la adopción de medidas preventivas en los familiares en riesgo
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Dušan, Vapa. "Varijabilnost mikrosatelitskih lokusa X hromozoma u populaciji Vojvodine." Phd thesis, Univerzitet u Novom Sadu, Medicinski fakultet u Novom Sadu, 2016. https://www.cris.uns.ac.rs/record.jsf?recordId=95598&source=NDLTD&language=en.
Full textAbstract:
Kratki uzastopni ponovci predstavljaju klasu mikrosatelitskih segmenata DNK, rasprostranjenih širom genoma čoveka. Građeni su od uzastopno ponavljajućih sekvenci dužine 2-6 parova nukleotida. Zahvaljujući različitom broju ponavljanja repetitivne jedinice, većina mikrosatelitskih markera pokazuje visok stepen polimorfizma dužine, koji je moguće ispitati primenom tehnike lančane reakcije polimeraze. Pored utvrđivanja spornih srodničkih odnosa, analiza X hromozom mikrosatelitskih markera može se uspešno koristiti i u oblastima kriminalistike, humane identifikacije, populaciono-genetičkim i demografskim istraživanjima i dr. Cilj istraživanja je izrada populacione studije, iz koje će se izračunati broj i frekvencija alela, struktura i frekvencija haplotipova, utvrditi vrednosti relevantnih statističkih parametara, oceniti mogućnost primene analize X-STR markera u slučajevima iz oblasti medicinske kriminalistike, humane identifikacije i veštačenja spornih srodničkih odnosa u populaciji Vojvodine. Istraživanjem je obuhvaćeno 200 odraslih, međusobno nesrodnih osoba. Izolacija DNK materijala iz krvnih mrlja vršena je Chelex metodom, a amplifikacija dobijenih uzoraka DNK metodom PCR, uz korišćenje komercijalnog Mentype® Argus X-12 PCR Amplification Kit – a. Razdvajanje i detekcija dobijenih fragmenata izvršeno je kapilarnom elektroforezom GeneScan i Genotyper programom. Statististička obrada rezultata izvršena je pomoću Arlequin i GENEPOP programa. Za vizuelizaciju interpopulacionih genetičkih odnosa, upotrebljen je program POPTREE2 i koordinatna analiza (Principal Coordinate Analysis - PCoA). Dobijeni rezultati ukazuju da se analiza ispitivanih X-STR markera može uspešno primeniti u slučajevima iz oblasti medicinske kriminalistike, humane identifikacije i veštačenja spornih srodničkih odnosa u populaciji Vojvodine, kao i da mogu poslužiti kao osnova za dalja istraživanja u populacionogenetičkim, antropološkim, demografskim i drugim oblastima.Short tandem repeats (STR) represent a class of microsatellites, widely spread throughout the human genome, consisting of tandemly repeated sequences of 2-6 bp. Related to variation in the number of repeat unit displayed, most of microsatellites show a high degree of length polymorphism, investigated by the PCR techniques. The aim of this research is to create a population study, which will be used to calculate allele and haplotype frequencies, determine the value of relevant statistical parameters and assess the possibility of applying X-STR markers analysis in the fields of forensics, human identification and kinship testing. The study included 200 unrelated adults. DNA isolation was performed by Chelex method and DNA amplification by PCR, using commercial Mentype Argus X-12 PCR Amplification Kit. Separation and detection of fragments was obtained by capillary electrophoresis using Gene Scanand Genotyper program. Statistical analysis of the result was performed using Arlequin and GENEPOP program. For visualization of inter population genetic distances POPTREE2 program and coordinate analysis (PCoA) was used. The results show that the analysis of X-STR markers can be successfully applied in the field of forensics, human identification and kinship testing in the population of Vojvodina, as well as to serve as a basis for further research in population genetic, anthropological, demographic and other scientific areas.
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Kasu, Mohaimin. "Validation and application of a highly discriminating and rapid 10-locus Y-STR DNA profiling system." University of the Western Cape, 2019. http://hdl.handle.net/11394/6760.
Full textAbstract:
Philosophiae Doctor - PhDDNA profiling the male specific region on the Y-chromosome is fundamental to forensic practise. Its recognised as a powerful analytical tool for investigation of sexual assault when the DNA evidence is highly admixed. Standard practises for processing sexual assault evidence include physically separate the sperm cell from the female fraction using differential extraction followed by autosomal DNA profiling. However, under specific scenarios of assault physical separation may not be possible due to the nature of the evidence. The research presented in this thesis was focused on the development and validation of the UniQTyper™ Y-10 prototype for male specific DNA profiling. The prototype which contains 10 Y-STR markers was developed and validated to deliver a rapid and cost-effective system while maintaining a forensic applicable level of performance. An allelic ladder is produced with an allele cloning approach for which an overview of the workflow and technicalities presented herein is aimed to assists an efficient bulk production process. In a second component novel sequence variation was reported across 153 sequenced alleles and submitted to Genbank. In this output the Y-STR panel was perused beyond the scope of length polymorphisms. In a proof of concept, its potential to discriminate between shared allele sizes by characterizing sequence structure variations is discussed. In a final component we generate the largest Y-STR survey across South Africa to establish reference data and to comprehensively assess the forensic genetics parameters for the UniQTyper™ Y-10.