INTRODUÇÃO: As aberrações cromossômicas constituem uma das maiores categorias das doenças genéticas, e são causa significativa do retardo mental e das malformações congênitas. Essas anormalidades correspondem a 50% dos casos de abortos espontâneos, 6% de natimortos e 0,6-1% de nativivos. OBJETIVO: Avaliar a freqüência das aberrações cromossômicas e classificar as principais aberrações encontradas nos pacientes atendidos em um serviço de Genética. CASUÍSTICA E MÉTODOS: Estudo retrospectivo de registros de resultados dos cariótipos de pacientes atendidos no Instituto da Criança no período 1992-2002. RESULTADOS: A freqüência de aberrações cromossômicas nos pacientes foi de 22% em 1122 cariótipos. As alterações numéricas foram 70,8% e 29,2% estruturais. A síndrome de Down foi a aberração numérica mais encontrada em 117/247 (47,4%) pacientes, e a segunda foi a síndrome de Edwards, em 18/247 (7,3%), seguida pela síndrome de Patau, que ocorreu em 9/247 (3,6%) pacientes. Entre as aberrações sexuais, a síndrome de Turner foi a mais freqüente, 18/247 (7,3%), seguida de três casos de triplo X, um de Klinefelter e um duplo Y. Dentre as aberrações estruturais, as deleções destacaram-se, com 27/247 (10,9%) dos casos; houve nove casos de síndrome de \"Cri-du-chat\" e oito de Wolf-Hirschhorn. CONCLUSÃO: A freqüência significativa de aberrações cromossômicas encontradas salienta como fundamental o uso do cariótipo de rotina nos pacientes atendidos no serviço de Genética, para definição diagnóstica e aconselhamento genético aos pacientes e seus familiares. / INTRODUCTION: Chromosomal disorders are included among the most important causes of genetic diseases with mental retardation and congenital malformation. Fifty percent of these abnormalities are spontaneously aborted and affect at least 6,0% of the stillbirth and the frequency in live births is 0.6%-1%. OBJECTIVE: To assess the frequency and the main of chromosomal disorders in patients assisted at a genetic service. CASUISTIC AND METHODS: A retrospective study was carried out regarding the record karyotype of patients assisted at Instituto da Criança within the period of 1992-2002. RESULTS: The frequency of chromosomal disorders of the patients was found in 22.0% among 1122 karyotypes. The numerical abnormalities among patients were 70.8% and 29.2% of them were structurals. Down syndrome was the most common numerical abnormality, found in 117/247 (47.4%) patients, followed by Edwards syndrome in 18/247 (7.3%) and Patau syndrome in 9/247 (3.6%) patients. Among the sexual abnormalities, Turner syndrome was the most common, in 18/247 (7.3%) patients, followed by three cases of triple X syndrome, one case of Klinefelter syndrome and a case of XYY syndrome. Among all structural abnormalities, the deletions were the most common, found in 27/247 (10.9%) of the cases, with 9 patients with \"Cri-du-chat\" syndrome and 8 cases of Wolf-Hirschhorn syndrome. CONCLUSION: The significance frequency of chromosome abnormalities emphasizes the importance of the G-banding karyotyping in the routine evaluation of patients assisted at the genetic service to attain a diagnosis definition and provide genetic counseling to the patients and family members.

Cancer is a leading cause of death worldwide, resulting in an estimated 1.6 million mortalities and 600,000 new cases in the US alone in 2015. Gene fusions, hybrid genes formed from two originally separated genes, are known drivers of cancer. However, gene fusions have also been found in healthy cells due to routine errors in replication. This project aims to understand the role of gene fusion in cancer. Specifically, we seek to achieve two goals. First, we would like to develop a computational method that predicts if a gene fusion event is associated with the cancer or healthy sample. Second, we would like to use this information to determine and characterize molecular mechanisms behind the gene fusion events. Recent studies have attempted to address these problems, but without explicit consideration of the fact that there are overlapping fusion events in both cancer and healthy cells. Here, we address this problem using FUsion Enriched Learning of CANcer Mutations (FUELCAN), a semi-supervised model, which classifies all overlapping fusion events as unlabeled to start. The model is trained using the known cancer and healthy samples and tested using the unlabeled dataset. Unlabeled data is classified as associated with healthy or cancer samples and the top 20 data points are put back into the training set. The process continues until all have been appropriately classified. Three datasets were analyzed from Acute Lymphoblastic Leukemia (ALL), breast cancer and colorectal cancer. We obtained similar results for both supervised and semi-supervised classification. To improve our model, we assessed the functional landscape of gene fusion events and observed that the pathway neighbors of both gene fusion partners are differentially expressed in each cancer dataset. The significant neighbors are also shown to have direct connections to cancer pathways and functions, indicating that these gene fusions are important for cancer development. Future directions include applying the acquired transcriptomic knowledge to our machine learning algorithm, counting transcription factors and kinases within the gene fusion events and their neighbors and assessing the differences between upstream and downstream effects within the pathway neighbors.

Made available in DSpace on 2017-07-21T19:59:45Z (GMT). No. of bitstreams: 1 Karina de Almeida Coelho.pdf: 3433585 bytes, checksum: 1e105f483478f4e2247d17b49c1eee4f (MD5) Previous issue date: 2014-02-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Basic and molecular cytogenetic studies were carried out in Apareiodon affinis (Parodontidae) of five populations: Passa Cinco River, Ipeúna – SP; Piracicaba River, Piracicaba – SP; Paraná River (lake of the Itaipu dam - Santa Helena – PR) all belong to Upper Paraná River hidrografic system and; two localities of the Paraguay River drainage, Cuiabá River, Cuiabá - MT and, Paraguay River, Cáceres - MT. The conventional analysis showed that the three populations of the Upper Paraná River system have 2n = 54 chromosomes to males and 2n= 55 chromosomes to females. Those differences in the chromosome number are due to by presence of sex chromosome system showing female heterogamety ZZ/ZW1W2 type. The karyotypic formula and fundamental number (FN) for these three populations was 50 m/sm + 4 st. FN = 108 to males and; 49 m/sm + 6 st, FN = 110 to females. The sex chromosomes Z was characterized as the largest metacentric, while the chromosome W1 and W2 appears to be subtelocentrics and have half the size of the Z chromosome. In turn, the population of the Cuiabá River, Cuiabá – MT have 2n = 54 chromosome to males and females, karyotypic formula 42 m/sm + 2 st + 10 a and FN = 98 and; the Paraguay River population show 2n = 54 chromosomes and no heteromorphic sex chromosomes system and, karyotypic formula 36 m/sm + 2st + 16 a. Fluorescence in situ hybridizations (FISH) com 18S and 5S ribosomal DNAs were performed in the different populations of A. affinis, resulting in (i) a single metacentric chromosome pair bearing 5S rDNA sites for the samples on the Upper Paraná River, (ii) a heteromorphic situation of a chromosome metacentric and one acrocentric for the population of the Cuiabá River and; (iii) a acrocentric pair bearing 5S rDNA sites for the population of the Paraguay River. The 18S rDNA was found in the terminal region of the long arm of a subtelocentric pair in all populations. This situation is considered a sinapomorfic feature in Parodontidae when compared with the sister group Anostomidae. FISH with pPh2004 satellite DNA was also performed in all the populations of this study showing positive hybridization in differential sites: 3-4 pairs all m/sm in the Upper Paraná River samples and; 6-8 st/a pairs in the Paraguay River samples. Thus, the cytogenetic differences observed between Upper Paraná and Paraguay Rivers populations is possible to affirm the occurrence of a high karyotipic differentiation in gene flow restriction. Lower cytogenetic differentiation can be observed also when compared samples from the same river system. Thus, is possible to state that A. affinis of the Upper Paraná River population is divergent and should have their taxonomic condition reviewed. / Estudos citogenéticos básicos e moleculares foram realizados em cinco populações de Apareidon affinis (Parodontidae): Rio Passa Cinco, Ipeúna – SP; Rio Piracicaba, Piracicaba – SP; Rio Paraná (lago da represa de Itaipu – Santa Helena – PR) pertencentes ao sistema hidrográfico do Alto Rio Paraná e duas populações da bacia do alto Rio Paraguai, rio Cuiabá, Cuiabá - MT e rio Paraguai, Cáceres - MT. A análise convencional mostrou que nas três populações do sistema alto rio Paraná apresenta 2n = 54 cromossomos para machos e 2n = 55 cromossomos para fêmeas. Esta diferença de número cromossômico é resultado da presença do sistema de cromossomos sexuais múltiplo com heterogamia feminina, do tipo ZZ/ZW1W2. A fórmula cromossômica e número fundamental para estas três populações foi 50 m/sm + 4 st, NF = 108 para machos e; 49 m/sm + 6 st, NF = 110 para fêmeas. O cromossomo sexual Z é caracterizado por ser o maior cromossomo metacêntrico do complemento, enquanto os cromossomos W1 e W2 são subtelocêntricos com metade do tamanho do cromossomo Z. A população do rio Cuiabá, por sua vez, possui 2n = 54 cromossomos para machos e fêmeas, fórmula cromossômica 42 m/sm + 2 st + 10 a e; NF = 98 e a população do rio Paraguai não apresenta heteromorfismo de cromossomos sexuais e fórmula cariotípica 36 m/sm + 2 st + 16 a. Hibridização in situ fluorescente (FISH) com DNAs ribossomais 18S e 5S foram realizadas nas diferentes populações de A. affinis, resultando em apenas um par cromossômico metacêntrico marcado com DNAr 5S para as populações do Alto Rio Paraná, uma situação heteromórfica com um cromossomo metacêntrico e um acrocêntrico para a população do rio Cuiabá e; um par acrocêntrico para a população do rio Paraguai. O DNAr 18S foi localizado na região terminal do braço longo de um par cromossômico subtelocêntrico, de todas as populações estudadas podendo ser considerado uma característica sinapomórfica para a família, quando comparada com o grupo irmão Anostomidae. FISH com DNA satélite pPh2004 isolado de Parodon hilarii também foi realizada nas populações dos sistemas hidrográficos do alto rio Paraná e bacia do rio Paraguai, evidenciando hibridação positiva em sítios diferenciais: 3 – 4 pares marcados, todos m/sm com divergência populacional no Alto Rio Paraná e, 6 – 8 pares marcados, também com divergência para as populações do rio Paraguai, em sua maioria acrocêntricos. Assim, levando em consideração as diferenças cromossômicas entre Alto Rio Paraná e Rio Paraguai é possível afirmar a existência a de uma alta diferenciação cariotípica entre as populações dos diferentes sistemas hidrográficos em isolamento de fluxo gênico. Diferenciação menor também pode ser constatada quando comparadas as localidades de um mesmo sistema hidrográfico. Deste modo, é possível afirmar que as populações de A. affinis do Alto Rio Paraná são divergentes, possibilitando que sua condição taxonômica seja revista.

In order to develop a stable strain of Bacillus megaterium for Keratinase production, the Keratinase gene (KerA) of Bacillus lichiniformis ATCC 53757 and SPlipA gene from plasmid pHIS1525.SPlipA (Bacillus megaterium origin) were PCR amplified and constructed to give a gene cassette called SPK . Then the gene cassette SPK was cloned into the Integration vector, pMUTIN-GFP+ 6192bps and transformed in Bacillus megaterium ATCC 14945. The chromosomal integration was created using homologous single crossing over mechanism. The strong natural promoter from the chromosomal locus of the SPK not only produced the increased extracellular enzyme, but also functions as a non inducible promoter which does not require any inducer for the production of the enzyme in the new integrant strain. The integrant strain was subjected to feather degradation test and found that it could totally digest the feather meal in complete seven days, resulting in a rich fermentation broth.

Le syndrome de Bloom (BS) est une maladie génétique rare caractérisée par une forte augmentation du taux d’échanges entre chromatides soeurs, des anomalies de ségrégation des chromosomes et une prédisposition au développement de tous types de cancers. Ce syndrome est la conséquence de mutations dans les deux copies du gène BLM, codant pour une 3’-5’ ADN hélicase de type RecQ. La ou les fonctions de la protéine BLM sont encore mal définies mais les données de la littérature convergent vers un rôle de BLM dans des mécanismes de surveillance et/ou maintien de l’intégrité du génome. La protéine BLM serait impliquée dans le redémarrage de fourches de réplication bloquées pendant la phase S et serait nécessaire à la résolution de ponts anaphasiques en mitose, notamment de ponts particuliers appelées « UltraFine anaphase Bridges » (UFBs). Ces UFBs, qui relient les chromatides soeurs entre elles, ne sont pas détectables par les colorants classiques et leur présence ne peut-être révélée que par la détection des protéines PICH (Plk1-Interacting Checkpoint Helicase) ou BLM. A l’état basal, ces UFBs sont essentiellement d’origine centromérique (cUFBs).Tout l’enjeu de mon projet était de déterminer si BLM était également impliquée dans la prévention de la formation de ces cUFBs et donc si BLM jouait un rôle avant l’anaphase. Nous avons montré que BLM est recrutée aux centromères de la phase G2 jusqu’en mitose. BLM, en coopération avec la protéine PICH, est nécessaire (1) à l’organisation structurale de l’ADN centromérique, (2) à la disjonction complète des centromères, indépendamment de la voie des cohésines, suggérant une implication de ces protéines dans le processus de décaténation des centromères et (3) au recrutement de la topoisomérase IIa (Topo IIa) active aux centromères.Nos résultats révèlent ainsi une nouvelle localisation et une nouvelle fonction de la protéine BLM aux centromères et montrent pour la première fois l’implication des protéines BLM et PICH dans la décaténation centromérique avant l’anaphase. Nous proposons que BLM et PICH, par leurs activités respectives hélicase et de remodelage de la chromatine, modifient la structure des centromères pendant la pré-métaphase, rendant ainsi certaines caténations accessibles à la Topo IIa avant l’anaphase. La défaillance de ce mécanisme entraînerait la persistance de caténations centromériques non résolues avant l’anaphase. Ainsi, dans les cellules BS, la fréquence élevée de cUFBs aurait deux origines différentes : une partie correspondrait à des cUFBs formés du fait d’une décaténation défaillante des centromères avant l’anaphase, et l’autre partie correspondrait à des cUFBs « physiologiques » non résolus en anaphase. Afin de distinguer l’origine des cUFBs, nous avons appelé ceux issus de caténations non résolues avant l’anaphase les UFBs centromériques surnuméraires (SC-UFBs pour Supernumerary Centromeric UFBs). / Bloom syndrome (BS) is a rare genetic disease characterized by a sharp increase in the rate of sister chromatid exchanges, chromosome segregation abnormailities and a predisposition to the development of all types of cancers. This syndrome is caused by mutations in both copies of the BLM gene, which encodes BLM, a RecQ 3'-5 DNA helicase. The specific function(s) of BLM remain unclear, but the data from the literature converge towards a role for BLM in mechanisms monitoring and / or maintaining genome integrity. The BLM protein may be involved in restarting stalled replication forks during S phase and necessary to resolve anaphase bridges in mitosis, including particular bridges called "Ultrafine Anaphase Bridges" (UFBs). These UFBs, which link sister chromatids together, are not detectable by conventional stains and their presence can only be revealed by the detection of the proteins PICH (PLK1-interacting checkpoint helicase) or BLM. In untreated cells, UFBs originate mostly from centromeres (cUFBs).The challenge of my project was to determine whether BLM was also involved in preventing the formation of cUFBs and so, if it played a role before anaphase.We showed that BLM is recruited at centromeres from G2 phase to mitosis. BLM, in cooperation with PICH, is required for (1) structural organization of centromeric DNA, (2) completion of centromere disjunction, independently of the cohesin pathway, suggesting an involvement of these proteins in centromere decatenation process, and (3) recruitment of active topoisomerase IIα (Topo IIα) to centromeres. Thus, we report a new localization and a new function of BLM at centromeres, revealing for the first time a new role for BLM and PICH in a previously unknown centromeric decatenation mechanism, crucial for complete centromere disjunction.We propose that the combined action of BLM and PICH promotes, through their helicase and chromatin remodelling activities, respectively, the organization of centromeric chromatin, thereby rendering some centromeric catenates accessible to Topo IIa before the onset of anaphase. The failure of this mechanism may lead to the persistence of some centromeric catenations not resolved before anaphase. Thus, the increase in the frequency of centromeric UFBs in BLMdeficient cells has two different origins: cUFBs arising from catenations not resolved before anaphase and physiological cUFBs not processed at anaphase onset. Two distinguish the two cUFB origins, we defined the former as supernumerary centromeric UFBs (SC-UFBs).

Human pluripotent stem cells are increasingly used for cell-based regenerative therapies worldwide, with the use of embryonic and induced pluripotent stem cells as potential treatments for a range of debilitating and chronic conditions. However, with the level of chromosomal aneuploidies the cells may generate in culture, their safety for therapeutic use could be in question. This study aimed to develop sensitive and high-throughput assays for the detection and quantification of human pluripotent stem cell aneuploidies, to assess any changes in their positioning in nuclei, as well as investigate the possible roles of lamins in the accumulation of aneuploidies. Using Droplet Digital PCR™, we optimised the detection of aneuploid cells in a predominantly diploid background. An assay was established for the sensitive detection of up to 1% of mosaicism and was used for the monitoring of low-level chromosome copy number changes across different cell lines, conditions and passages in the human pluripotent stem cells. In addition, fluorescence in-situ hybridisation was used to map genes ALB and AMELX on chromosomes 4 and X, respectively, in karyotype-stable chromosome X aneuploid lymphoblastoid cell lines. Our results demonstrated significant alternations in the gene loci positioning in the chromosome X aneuploid cell lines. Using the same established method, the positioning of ALB and AMELX was monitored, alongside the genomic instability with ddPCR™, in the different human pluripotent stem cell lines, conditions and passage. We demonstrated a highly plastic nuclear organisation in the pluripotent stem cells with many changes occurring within a single passage. Furthermore, these results were not exclusive to a single cell line or condition, regardless of the presence or absence of feeder cells and of passage number, and the flexibility of the chromatin organisation remained throughout the duration of the study. We demonstrated high levels of genomic instability with recurrent gains and losses in the AMELX copy number in the human embryonic stem cells during the course of our study, however no significant changes in their gene loci positioning from these abnormalities were observed. xvi | P a g e Additionally, we observed reduced levels of lamin B2 in the aneuploid lymphoblastoid cell lines and complete loss in some hPSC samples. Our results support recent findings that suggest a link between lamin B2 loss and the formation of chromosome aneuploidies in cell culture. In conclusion, our data demonstrates several key novel findings. Firstly, we have established a sensitive technique for the detection of up to 1% mosaicism, which to our knowledge is the most sensitive assay currently available. Secondly, we showed significant changes in the gene loci positioning between aneuploid and diploid cell lines. Thirdly, utilising our novel ddPCR™ assay, we demonstrated the karyotypical instability of hPCSs with consistent gains and/or loses of gene copy numbers in a short period of time in culture. When studying the effects of different growth conditions, we showed that the karyotypical instability was not exclusive to a single condition or a combination of conditions, and what is more, the karyotypical abnormalities detected were not observed to change the gene positioning of hPSCs significantly, with the genome organisation remaining plastic. Finally, our results support a potential association of lamin B2 loss and karyotypical instability. We conclude that more sensitive and robust techniques need to be readily used by clinicians for the screening of potential therapeutic hPSCs.

Disrupted in schizophrenia 1 (DISC1), located on chromosome 1, was first identified due to its disruption by a chromosomal translocation, t(1;11)(q42;q14). This translocation co-segregates with psychiatric illness in the Scottish family within which it was discovered. DISC1 is a component of the mitochondrial trafficking machinery and regulates trafficking of mitochondria in neurons, possibly implicating defective mitochondrial trafficking as a contributory factor in psychiatric illness. The product of another candidate gene for psychiatric illness, Glycogen synthase kinase 3β (GSK3β), is known to interact directly with DISC1 and has also been reported to be involved in mitochondrial trafficking. The interaction of these proteins has not been investigated in this process. The work in this thesis centres around a novel mouse model of the t(1:11) translocation. I use time-lapse imaging of live cells to show that hippocampal neurons cultured from this mouse model exhibit altered axonal mitochondrial trafficking, including reduced mitochondrial pausing. I also demonstrate that the DISC1 interactor GSK3β is a component of the mitochondrial trafficking machinery and investigate effects of the t(1:11) event upon this multi-protein complex. Finally, I demonstrate altered mitochondrial motility responses to overexpression of GSK3β in mutant neurons. Defective mitochondrial trafficking, particularly reduced pausing, could result in an altered distribution of mitochondria within neurons, leading to an impaired ability to respond to cellular conditions, such as the requirement to power synaptic vesicle release or the ion pumps that restore membrane potential following action potential generation. This could ultimately affect neuron viability, leading to brain dysfunction. My data therefore support a proposed disease mechanism whereby defective mitochondrial trafficking contributes to susceptibility to psychiatric illness in carriers of the t(1:11) translocation, and may be relevant to psychiatric illness in general.

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No. of bitstreams: 2 merged.pdf: 2827460 bytes, checksum: 84c579b817b24021e72bdea116e8ab88 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-03-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Intellectual disability is a signal comprising a set of clinically and genetically heterogeneous disorders in which the development and/or function of the brain is compromised. This deficiency is characterized by significant limitations both in intellectual functioning and in adaptive behavior and is observed begins before 18 years of age. It is characterized by a high degree of variable expression, and the expression of a wide range of phenotypes, ranging from various genetic syndromes known to characteristics non-syndromic and psychological and/or psychiatric disorders. The etiology is still poorly understood and about half of the cases are unclear. In recent years, the chromosomal analysis by microarray has revolutionized the evaluation of patients with developmental delay or intellectual disability. By this method, the genome of a patient is examined to detect gains or losses of genetic material that are usually too small to be detected by chromosome banding studies. Genomic deletions and duplications have an important role in characterizing genetic diseases, including many neurological disorders and neural development. Identifying these changes may contribute to the clinical management of affected individuals and assist their families, and furthermore, can provide information on the processes of development and brain function. In this context the main objective of this study was identified possible submicroscopic genomic changes associated with intellectual disability, using a platform Chromosomal Microarray high resolution in patients referred by doctors of public health from Goiás state and had initially a normal karyotype. Thus 15 patients with intellectual disabilities were tested by high resolution HD CytoScan Array (Affymetrix) tecnology which detected the presence of 33 variations in the number of genome copies in 10 (66.7%) of the probands. Nineteen microduplications (57.6%) and 14 microdeletions (42.4%) were observed, and 17 CNVs (51.5%) were neutral, 7 (21.2%) pathogenic, 5 (15.15%) potentially pathogenic and 4 (12.12%) of uncertain significance. Five patients showed no change in the number of copies. In this study, we could propose a genetic etiology for the phenotype of 8 patients and thus the diagnostic yield of the platform used was 53.3%. Although modest, this study was significant because this technology was first employed in the state of Goiás and thus, could contribute more genetic information about this complex and heterogeneous neurological sign of great importance to global public health. / A deficiência intelectual é um sinal que compreende um conjunto de distúrbios clinica e geneticamente heterogêneos em que o desenvolvimento e/ou a função do cérebro é comprometida. Esta deficiência é caracterizada por limitações significativas tanto no funcionamento intelectual quanto no comportamento adaptativo e se inicia antes dos 18 anos de idade. É caracterizada por um elevado grau de expressividade variável, e pela manifestação de uma grande gama de fenótipos, variando de diversas síndromes genéticas conhecidas a características não sindrômicas e desordens psicológicas e/ou psiquiátricas. A etiologia ainda é mal compreendida e cerca de metade dos casos não são esclarecidos. A análise cromossômica por microarray tem revolucionado, nos últimos anos, a avaliação de pacientes com atraso no desenvolvimento ou deficiência intelectual. Por este método, o genoma de um paciente é examinado para a detecção de ganhos ou perdas de material genético que, normalmente, são muito pequeno para serem detectados por estudos cromossômicos com bandamento G. Deleções e duplicações genômicas têm um papel importante na caracterização de doenças genéticas, incluindo muitas desordens neurológicas e do desenvolvimento neural. A identificação dessas alterações pode contribuir para a manejo clínico dos indivíduos afetados e auxiliar suas famílias, e além disso, pode também fornecer informações sobre os processos do desenvolvimento e funcionamento do cérebro. Neste contexto o objetivo principal deste estudo foi identificar possíveis alterações genômicas submicroscópicas associadas à deficiência intelectual, utilizando uma plataforma de Chromosomal Microarray de alta resolução, em pacientes referenciados por médicos da rede pública de saúde do Estado de Goiás e que tenham apresentado inicialmente um cariótipo normal. Desta forma foram testados 15 pacientes com deficiência intelectual, pela tecnologia de alta resolução CytoScan HD Array (Affymetrix) que detectou a presença de 33 variações no número de cópias genômicas em 10 (66,7%) dos probandos. Foram observadas 19 microduplicações (57,6%) e 14 microdeleções (42,4%), sendo que 17 CNVs (51,5%) eram neutras, 7 (21,2 %) patogênicas, 5 (15,15%) potencialmente patogênicas e 4 (12,12%) de significado incerto. Cinco pacientes não apresentaram nenhuma alteração no número de cópias. Neste estudo foi possível propor uma etiologia genética para o fenótipo de 8 pacientes e dessa forma o rendimento diagnóstico, a título de pesquisa, da plataforma utilizada foi de 53,3%. Este estudo foi relevante já que esta tecnologia foi empregada pela primeira vez no estado de Goiás e com isso, pudemos contribuir com mais informação genética sobre esse complexo e heterogêneo sinal neurológico de grande importância para a saúde pública mundial.

INTRODUÇÃO: As aberrações cromossômicas constituem uma das maiores categorias das doenças genéticas, e são causa significativa do retardo mental e das malformações congênitas. Essas anormalidades correspondem a 50% dos casos de abortos espontâneos, 6% de natimortos e 0,6-1% de nativivos. OBJETIVO: Avaliar a freqüência das aberrações cromossômicas e classificar as principais aberrações encontradas nos pacientes atendidos em um serviço de Genética. CASUÍSTICA E MÉTODOS: Estudo retrospectivo de registros de resultados dos cariótipos de pacientes atendidos no Instituto da Criança no período 1992-2002. RESULTADOS: A freqüência de aberrações cromossômicas nos pacientes foi de 22% em 1122 cariótipos. As alterações numéricas foram 70,8% e 29,2% estruturais. A síndrome de Down foi a aberração numérica mais encontrada em 117/247 (47,4%) pacientes, e a segunda foi a síndrome de Edwards, em 18/247 (7,3%), seguida pela síndrome de Patau, que ocorreu em 9/247 (3,6%) pacientes. Entre as aberrações sexuais, a síndrome de Turner foi a mais freqüente, 18/247 (7,3%), seguida de três casos de triplo X, um de Klinefelter e um duplo Y. Dentre as aberrações estruturais, as deleções destacaram-se, com 27/247 (10,9%) dos casos; houve nove casos de síndrome de \"Cri-du-chat\" e oito de Wolf-Hirschhorn. CONCLUSÃO: A freqüência significativa de aberrações cromossômicas encontradas salienta como fundamental o uso do cariótipo de rotina nos pacientes atendidos no serviço de Genética, para definição diagnóstica e aconselhamento genético aos pacientes e seus familiares. / INTRODUCTION: Chromosomal disorders are included among the most important causes of genetic diseases with mental retardation and congenital malformation. Fifty percent of these abnormalities are spontaneously aborted and affect at least 6,0% of the stillbirth and the frequency in live births is 0.6%-1%. OBJECTIVE: To assess the frequency and the main of chromosomal disorders in patients assisted at a genetic service. CASUISTIC AND METHODS: A retrospective study was carried out regarding the record karyotype of patients assisted at Instituto da Criança within the period of 1992-2002. RESULTS: The frequency of chromosomal disorders of the patients was found in 22.0% among 1122 karyotypes. The numerical abnormalities among patients were 70.8% and 29.2% of them were structurals. Down syndrome was the most common numerical abnormality, found in 117/247 (47.4%) patients, followed by Edwards syndrome in 18/247 (7.3%) and Patau syndrome in 9/247 (3.6%) patients. Among the sexual abnormalities, Turner syndrome was the most common, in 18/247 (7.3%) patients, followed by three cases of triple X syndrome, one case of Klinefelter syndrome and a case of XYY syndrome. Among all structural abnormalities, the deletions were the most common, found in 27/247 (10.9%) of the cases, with 9 patients with \"Cri-du-chat\" syndrome and 8 cases of Wolf-Hirschhorn syndrome. CONCLUSION: The significance frequency of chromosome abnormalities emphasizes the importance of the G-banding karyotyping in the routine evaluation of patients assisted at the genetic service to attain a diagnosis definition and provide genetic counseling to the patients and family members.

Chicken is a major protein source and intensively selected for economically important traits by humans. As such, this generated a huge range of phenotypes that representing a diverse spectrum of genetic variation. Understanding the functional basis of the genetic variants that underlie these traits, however, remains a formidable endeavour particularly for complex traits. Nonetheless, molecular phenotyping of an organism from sequenced data is doable with the advances in bioinformatics analysis and unparalleled surveys of genome wide genetic variants. This provides the opportunity to gain insights into the genome architecture and assists in identifying chromosomal regions underlying selection through a “sequences to consequences” approach. Combining a whole genome re-sequencing (WGS) approach with the knowledge of selection history, this thesis aimed to study the chromosomal regions and genetic variants underlying traits of interest in various selected chicken populations. To achieve this, genetic (quantitative and population genetics), genomic and bioinformatics approaches were employed and integrated to investigate the genome wide selection signatures in a number of different lines of chicken selected for different complex traits. This includes analysing: (i) divergently selected broilers for fatness traits (Chapter 2), (ii) a closed population of layer chickens (Chapter 3), (iii) selection signatures unique to broiler or layer chickens (Chapter 4) and (iv) selection signatures in colony stimulating factor 1 (CSF1) associated with gene expression differences in broiler and layer populations (Chapter 5). Candidate genes and nucleotides underlying potential selection regions were identified, and attempts were made to further elucidate the potential interplay between genes and the biological pathways involved in regulating traits in these selected chicken lines. Incorporating integrative approaches, variants within selection signatures were annotated to provide further evidence of their functional consequences. Overall, non-coding regions were enriched in selection signatures implied that causative variants may have regulatory roles. Capitalising on the millions of genetic variants discovered from WGS, chromosomal regions subject to selection were detected using a number of population genetics statistics. In broiler chicken lines divergently selected for very low-density plasma lipoprotein (VLDL) (Chapter 2), incorporating signatures of selection helped to improve the resolution of previously mapped quantitative traits loci (QTL) intervals. This research demonstrated that the integration of the analysis of selection signatures with functional annotation of genetic variants enabled refinement and characterisation of the QTL for fatness traits. In a closed population of brown leghorn layers (Chapter 3), evidence of selection signatures was found through Tajima’s D analysis. The analysis unravelled selection signatures encoding genes involved in numerous pathways and genes having key roles such as in behaviour, including feather pecking. Combining population differentiation statistic (FST) and Tajima’s D, a number of regions subject to divergent selection between broilers and white egg layers were identified (Chapter 4). Selection signatures were found to harbour mutations involved in cellular and tissue development, including genes having important roles in growth, fatness, egg shell strength and muscle development. These regions and the overlapping genes thereby may be potentially contributing to the different phenotypic variations observed between broilers and layers. In Chapter 5, a revised gene model for colony stimulating factor 1 (CSF1) showing complex pattern of alternate transcripts was predicted from transcriptome analysis of RNA isolated from 21 different tissues. In parallel, selection signatures analysis with the FST statistic, identified selection signatures that differentiate broilers to white egg layers (3 regions) or brown egg layers to white egg layers (4 regions). All these selection signatures were located within non-coding regions, indicating potential divergent selection of CSF1 within regulatory regions. Overall, the results presented in this thesis using the “sequences to consequences” approach, link several genomic regions and genes to phenotypic variation in domesticated chicken lines. The work reported here serves as a foundation for further study to decipher the relationship between “genotype and phenotype” and its functional consequences due to selection.