Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2016-10-10T12:36:43Z No. of bitstreams: 1 TeseGHM.pdf: 1501036 bytes, checksum: c01a6f35eb3f6b3347f3be5bfed6db93 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2016-10-11T14:25:20Z (GMT) No. of bitstreams: 1 TeseGHM.pdf: 1501036 bytes, checksum: c01a6f35eb3f6b3347f3be5bfed6db93 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2016-10-11T14:25:28Z (GMT) No. of bitstreams: 1 TeseGHM.pdf: 1501036 bytes, checksum: c01a6f35eb3f6b3347f3be5bfed6db93 (MD5) / Made available in DSpace on 2016-10-11T19:59:44Z (GMT). No. of bitstreams: 1 TeseGHM.pdf: 1501036 bytes, checksum: c01a6f35eb3f6b3347f3be5bfed6db93 (MD5) Previous issue date: 2015-01-16 / Não recebi financiamento / The analysis of DNA for the purpose of obtaining genetic profile has become essential for criminal investigation and judicial procedure. Since the origins of the techniques of human identification, nothing has been discovered with greater discriminatory power, between two randomly chosen individuals. Genetic proof has assumed great importance in the courts, however, for the operators of law this whole theme is cloaked in great mystery. The objective of this study was to obtain, and to offer to the operators of Law, a general view on the utilization of genetic profiles, and their consequences for the system, and Brazilian society. However, this powerful tool of human identification, DNA and its interconnections, has been thrust forward by very recent advances, in such volume as to alter in a significant way procedures and results, being obliged to follow the paths beaten by scientists, for a simplified form to put into order the information which has directed the forensic genetics to it's current point in time. A review of human identification was made until the discovery of DNA, its structure, evolution and development. The procedures and the various techniques were analyzed, which were being perfected for the obtaining results from the collecting of biological traces at the crime scene to the laboratory analysis, culminating with automatization by PCR and the elaboration of a genetic profile. DNA in the Forensic world, it's birth and consecration were examined. The presence of the instruments available for working the markets, bestowing greater means of discrimination, the STR tests, the future of the SNPs, the sequence of the second generation, and the obtaining of phenotypic characteristics, were duly dealt with. It was analysed, since its origin and implantation up to the current time, the working of the more significant Genetic Profile Data Banks, its technical and legal concerns, as well as the situation in Brazil, with its advances and obstacles, to become part of the forensic DNA community. Experiments in the testing of carbonized human bones were carried out, for identification in criminal procedure, with full details of the materials utilized, methodology, laboratory equipment and software for analyzing the results, ending up with a conclusive result. Following on the exploratory part was carried out through visits to the most expressive world DNA centres, located in the USA, France, the United Kingdom and Brazil, aimed at by means of interviews to discuss this topic, from technical to ethical aspects, and of the data banks to the operations of the system. Finally, in the discussion, the points observed in the centres of excellence, the results of the interviews, and the possible advantages of each system, in a totally fractioned global posture, were addressed. / A análise do DNA com a finalidade de obtenção de perfil genético tornou-se imprescindível para a investigação criminal e a persecução judicial. Desde os primórdios das técnicas de identificação humana, nada havia sido descoberto com maior poder discriminatório entre dois indivíduos escolhidos ao acaso. A prova genética assumiu grande importância nos tribunais, no entanto, para os operadores do direito, toda essa temática se reveste de grande mistério. O objetivo deste estudo foi obter, e poder oferecer aos operadores do Direito, uma visão geral sobre a utilização de perfis genéticos, e suas consequências para o sistema e a sociedade brasileira. No entanto, essa poderosa ferramenta de identificação humana, o DNA e suas interligações, vêm sendo impulsionada por recentíssimos avanços, de tal monta a alterar de forma significativa procedimentos e resultados, obrigando percorrer os caminhos trilhados pelos cientistas, para de forma simplificada ordenar as informações que nortearam a genética forense até nossos dias. Fez-se uma revisita à identificação humana, até a descoberta do DNA, sua estrutura, evolução e desdobramento. Foram analisados os procedimentos, e as várias técnicas, que foram sendo aperfeiçoadas, para obtenção de resultados desde a coleta de vestígios biológicos na cena do crime, até a análise laboratorial, culminando com a automatização pela PCR e a elaboração de um perfil genético. Examinou-se o DNA no mundo Forense, seu nascimento e consagração. A presença do instrumental à disposição para trabalhar marcadores, conferindo maior poder de discriminação, o exame dos STRs (Short Tandem Repeats), o futuro com SNPs, o sequenciamento de segunda geração e a obtenção de características fenotípicas foram devidamente abordadas. Verificou-se, desde sua origem e implantação até nossos dias, o funcionamento dos Bancos de Perfis Genéticos mais significativos, sua problemática técnica e legal, assim como a situação do Brasil, com seus avanços e entraves para fazer parte da comunidade forense do DNA. Realizou-se experimentalmente o exame de ossos humanos carbonizados, para identificação em procedimento criminal, com detalhamento dos materiais utilizados, metodologia, equipamentos laboratoriais e software para análise de resultados, finalizando com resultado conclusivo. Na parte exploratória vivencial deste trabalho, foram realizadas visitas aos mais expressivos centros mundiais de DNA, localizados no EUA, França, Reino Unido e Brasil, objetivando por meio de entrevistas discutir a temática, da técnica à ética, e dos bancos de dados à operacionalidade do sistema. Finalmente, na discussão foram abordados os pontos observados nos centros de excelência, o resultado das entrevistas, e as possíveis vantagens de cada sistema, em uma totalmente fracionada postura global.

Em 2012, o Brasil aprovou a lei 12.654 que regulamenta o uso dos bancos de perfis genéticos para fins de investigação criminal. Esta lei é um dos marcos nas discussões acerca do uso do DNA nas investigações criminais que se intensificaram no país a partir de 2009 quando o FBI doou ao Brasil o Combined DNA Index System (CODIS). A chegada dos bancos de dados de DNA ao Brasil faz parte de um processo de expansão internacional de bancos nacionais de perfis genéticos. Esta tese trata do processo de introdução desta tecnologia no Brasil. Através de entrevistas com especialistas de diferentes áreas, tais como perícia criminal, direito e bioética, da observação e participação em seminários e congressos de perícia criminal e das discussões travadas em publicações de revistas científicas esta pesquisa busca uma compreensão etnográfica dos nexos entre ciência, direito, tecnologia, segurança e poder em torno do processo de introdução dos bancos de perfis genéticos no Brasil. Na primeira parte, a tese descreve algumas relações e significados que fizeram a identificação genética vir a ser sinônimo de precisão científica acerca da identificação humana e o deslizamento para sua aplicação nas investigações criminais. Na segunda parte, aborda os primeiros efeitos do processo de introdução da tecnologia de bancos de perfis genéticos no Brasil a partir do processo de elaboração da lei dos bancos de DNA, da emergência de novas trajetórias de peritos criminais em genética forense e de alguns desafios do cotidiano da coleta, análise e armazenamento dos vestígios da cena do crime. Conhecer e entender como são colocadas em prática as diversas mediações que envolvem a estabilização do banco de DNA para fins de investigação criminal no Brasil permite refletir como a relação entre tecnociência, direitos, cidadania e políticas de segurança implicam em opções técnicas, éticas e políticas. / In 2012, Brazil approved the Federal Law 12.654, which regulates the use of genetic profiles for criminal investigations. Such law is one of the main landmarks in discussions concerning the use of DNA in criminal investigations that have intensified across the country since 2009, when the FBI donated to Brazil the Combined DNA Index System (CODIS). The arrival of these databases in Brazil is part of an international expansion process of national genetic profiles databases. This dissertation is about the introduction process of such biotechnology in Brazil. Through interviews with specialists from different areas, such as forensic sciences, law and bioethics, from observation and participation in forensics seminars and congresses and from discussions set in scientific publications this research aims for an ethnographic understanding of the nexus between science, law, technology, security and power around the introductory process of the genetic profile databases in Brazil. In its first part, the dissertation describes some relations and meanings that made genetic identification become a synonym of scientific precision concerning human identification and the transition for its application in criminal investigation. In its second part, it approaches the first effects of the introductory process of the technology in Brazil through the DNA database’s law elaboration process, from the emergency of new trajectories of genetic forensic experts and from a few challenges of the daily collection, analysis and storage of evidences of the crime scene. To know and to understand the mediations involved in the stabilization of the DNA databases for criminal investigation allow us to reflect on how the relation between technoscience, law, citizenship and safety politics affects and engenders technical options, ethics and policies.

Indiana University-Purdue University Indianapolis (IUPUI) / In the past, the present and the future, Lebanon has been an important link between the East and the West. It was always known as the ‘Switzerland of the East’. Over the years, it was a hotspot for different civilizations that uniquely shaped the genomic backbone of the current Lebanese. It is also a good representation of genetically admixed individuals with diverse phenotype characteristics and unique features. Lebanon, quite like other Middle Eastern populations, lacks sufficient genetic studies that helps to better comprehend the complex genomic composition of different traits and diseases. The lack of good representation of the Middle East and North Africa (MENA) region in global studies has led to ambiguity in discovering special ancestry markers and patterns in the Lebanese genome. Yet, in this study, a thorough investigation into a Lebanese collection shows new patterns that potentially would be helpful in forensic and genealogical applications. The investigation into the autosomal and Y-STRs revealed unique alleles that would be valuable in future forensic investigation analysis. In addition, the assessment of phenotype prediction models to predict eye, hair and skin color showed promising results in terms of prediction performance. Those results encourage the future use of intelligence tools in the regions that in return would aid in serving justice and furthering science research. In fact, ancestry and genetic distance studies confirms the presence of admixture within Lebanon between Europe and North Africa. / 2029-06-01

Criminology is a science dealing with the protection of citizens and state from infringement. Criminology uses mostly biological or genetic methods for crime detection. Forensic traces which are collected by forensic experts on the scene are the key items of those methods. Forensic genetics is among the most important forensic subdisciplines. Forensic genetics uses DNA analysis for identification. The main aims of this study are description and importance of biological, anthropological and genetic methods in criminology, different ways of forensic identification, division and collection of forensic traces, characterization and course of forensic DNA analysis and DNA profiling. Key words Criminology, forensic methods, forensic identification, forensic trace, forensic biology, anthropology and genetics, information systems, forensic DNA analysis, DNA profile.

Die Haplotypspezifische Extraktion (HSE) bietet für die Analyse von männlichen Mischprofilen einen neuen und direkteren Lösungsansatz, in dem die haploiden Y-chromosomalen DNS-Komponenten der einzelnen Individuen bereits vor der Analyse der individual spezifischen Marker separiert werden können und dadurch eine wirkliche physische Trennung erreicht wird. Die HSE verwendet Y-chromosomalen SNPs für die Erstellung allelspezifische Extraktionssonden, die nun gezielt nur die Marker der extrahierten DNS Komponente bzw. einer Person separieren sollen. Dabei werden im Hybridisationsschritt der HSE selektive nur komplett hybridisierte Sonden durch eine Polymerase verlängert. Während der Elongation erfolgt eine Biotinylierung des neu entstehenden Stranges, welcher dann selektiv durch Streptavidin markierte Eisenkügelchen extrahiert werden kann. Erste Durchführungen einer HSE zeigten nur eine sehr schwache bis keine Anreicherung. Während der Optimierung verschiedener Parameter wurde die Schlüsselstellung des Sondendesigns in der HSE-Technik deutlich. Die Ergebnisse zeigten, dass die neu entwickelten Sonden den Trennungserfolg der Mischprobe enorm verbessern und in einigen Fällen sogar zum Ausschluss des konkurrierenden Allels führten. Ein Vergleich der HSE Ergebnisse mit den simulierten Sondenparametern der getesteten Sonden ergab, dass der Extraktionserfolg der Sonde maßgeblich durch das Zusammenspiel von Sondenlänge und GC-Gehalt bestimmt wird. Durch dieses neu gewonnene Verständnis über den Einfluss der einzelnen Sondenparameter auf den Trennungserfolg der Mischprobe, können für künftige HSE Anwendungen Sonden effizienter erstellt und deren Wirksamkeit vorhergesagt werden. Zusätzlich konnte das neu entwickelte Vorhersage-Model der Sondenspezifität auch für weitere Extraktionsorte außerhalb des Y-Chromosoms bestätigt werden. Weiterhin konnte durch die Kombination verschiedener Sonden in einer Multiplex HSE mehrerer Y-chromosomaler Marker gleichzeitig getrennt. / Haplotype-specific extraction (HSE) allows the separation of diploid samples in their haploid components and offers in forensic a new straight forward method to separate Y-chromosomal mixed profiles, consisting of haplotype markers like short tandem repeats (STRs). The advantage of the HSE approach in mixture analysis is the real physical separation of the individual DNA components before the amplification of the STR markers. In order to use the HSE technique for the separation of male DNA mixtures, Y-chromosomal extraction probes were designed to single nucleotide polymorphisms (SNPs), which have been specific for one contributor of the male DNA mixtures. During extraction only complete matched probes are extended by a polymerase which results in the incorporation of biotinylated nucleotides. The synthesized and biotin labeled strand is separated by streptavidin coated magnetic beads. Finally, samples were analyzed by PCR coupled capillary electrophoresis for the detection of the extracted STR markers. First tests of a Y-chromosomal specific extraction showed only little till no enrichment of the targeted alleles. Therefore optimization tests of different parameters were carried out, which revealed the probe design as the key factor of successful HSE. A comparison between simulated probe parameters and their extraction success in HSE showed that the HSE probe efficiency mainly depends of the relation of probe length and GC-contents. Because of the new gained knowledge about the influence of the probe-design on the separation success, probes for future HSE application can be developed faster and cost-effective. The new prediction model for probe-specificity was also successful tested for the extraction of other genome-loci. Furthermore, a multiplex HSE approach was used to separate several STR markers simultaneously in one extraction reaction and therefore achieved the separation of one contributor Y-chromosomal haplotype.

<div><div>In the forensic science community, there is a vast need for tools to help assist investigations when standard DNA profiling methods are uninformative. Methods such as Forensic DNA Phenotyping (FDP) and proteomics aims to help this problem and provide aid in investigations when other methods have been exhausted. FDP is useful by providing physical appearance information, while proteomics allows for the examination of difficult samples, such as hair, to infer human identity and ancestry. To create a “biological eye witness” or develop informative probability of identity match statistics through proteomically inferred genetic profiles, it is necessary to constantly strive to improve these methods. </div><div><br></div><div>Currently, two developmentally validated FDP prediction assays, ‘HIrisPlex’ and ‘HIrisplex-S’, are used on the capillary electrophoresis to develop a phenotypic prediction for eye, hair, and skin color based on 41 variants. Although highly useful, these assays are limited in their ability when used on the CE due to a 25 variant per assay cap. To overcome these limitations and expand the capacities of FDP, we successfully designed and validated a massive parallel sequencing (MPS) assay for use on both the ThermoFisher Scientific Ion Torrent and Illumina MiSeq systems that incorporates all HIrisPlex-S variants into one sensitive assay. With the migration of this assay to an MPS platform, we were able to create a semi-automated pipeline to extract SNP-specific sequencing data that can then be easily uploaded to the freely accessible online phenotypic prediction tool (found at https://hirisplex.erasmusmc.nl) and a mixture deconvolution tool with built-in read count thresholds. Based on sequencing reads counts, this tool can be used to assist in the separation of difficult two-person mixture samples and outline the confidence in each genotype call.<br></div><div><br></div><div>In addition to FDP, proteomic methods, specifically in hair protein analysis, opens doors and possibilities for forensic investigations when standard DNA profiling methods come up short. Here, we analyzed 233 genetically variant peptides (GVPs) within hair-associated proteins and genes for 66 individuals. We assessed the proteomic methods ability to accurately infer and detect genotypes at each of the 233 SNPs and generated statistics for the probability of identity (PID). Of these markers, 32 passed all quality control and population genetics criteria and displayed an average PID of 3.58 x 10-4. A population genetics assessment was also conducted to identify any SNP that could be used to infer ancestry and/or identity. Providing this information is valuable for the future use of this set of markers for human identification in forensic science settings. </div></div><div><br></div>

The advances in molecular biology have increased the production of enormous amount of genetic information in a small period of time. This capacity of data production motivated the researchers to increase the rhythm of their researches. This necessity demands the use of efficient softwares in order to manage these data. Besides this, it also demands the development of good softwares in order to assist the researchers in the task of analyzing the data and giving them a biological meaning in a brief space of time. This work proposes a software model that will support the study of Forensic DNA, whose main repository is the autossomic DNA. This software intends to support the researchers in the identification of condemned persons or persons that are suspected of a crime. It also intends to assist the researchers in the study of paternity and the search for disappeared persons. The results of this work will be applied in the Forensic DNA Laboratory of UFAL. The software modeled here has four modules study of paternity , criminal , disappeared people and the bank of populational frequencies . The modules were modeled independently from each other, considering the specifications related to the analysis of genetic links. The software was developed using the JAVA programming language together with PostgreSQL database. Both are free software and have an excellent relationship between cost and benefit usage / Fundação de Amparo a Pesquisa do Estado de Alagoas / Os avanços da biologia molecular vêm favorecendo a geração de uma enorme quantidade de informações genéticas em um tempo cada vez menor. Essa capacidade de geração de dados permite que os pesquisadores acelerem o ritmo de suas pesquisas, exigindo a utilização de ferramentas eficientes para o gerenciamento desses dados. Outra necessidade está relacionada com o desenvolvimento de ferramentas computacionais com capacidade de auxiliar na tarefa de análisar e dar um significado biológico a estes dados em um breve espaço de tempo para os pesquisadores. Este trabalho propõe a modelagem de um ambiente de apoio à análise e ao estudo do DNA Forense, cujo principal repositório seja o DNA autossômico. Este ambiente visa dar suporte a identificação de pessoas condenadas ou suspeitas de ter realizado algum tipo de crime contra a sociedade, bem como auxiliar no estudo de paternidade e na busca de pessoas desaparecidas. Este ambiente irá atender ao Laboratório de DNA Forense, da UFAL, que vêm realizando estas atividades. O modelo do ambiente aqui proposto, possui quatro módulos, estudo de paternidade , criminal , desaparecido e o banco de freqüência das populações . Os módulos foram modelados de forma que funcionem independentemente, atendendo as especificações inerentes à análise sobre vínculo genético. O sistema foi desenvolvido na linguagem de programação JAVA com banco de dados PostgreSQL. Ambas as ferramentas possuem característica de software aberto e uma relação custo/benefício excelentes