Os transtornos do espectro autista (TEA) são condições neuropsiquiátricas caracterizadas por padrões comportamentais estereotipados, ausência ou limitação de comunicação verbal e de interação social recíproca. Diversos estudos têm mostrado que esses transtornos possuem etiologia genética complexa e heterogênea, o que dificulta a identificação dos fatores causais. Estima-se que cerca de 70% dos casos de TEA são idiopáticos. Portanto, com o objetivo de identificar mecanismos etiológicos associados aos TEA, utilizamos as seguintes estratégias: customização de uma lâmina de microarray CGH que possibilite a detecção não só de grandes CNVs, mas também de alterações menores do que 10 kbp, em exons e regiões UTR de genes potencialmente candidatos; a comparação entre os tipos de rearranjos detectados em pacientes sindrômicos e em não sindrômicos e, ainda, a investigação mais detalhada de uma família com indivíduos portadores de transtorno autista e síndrome de Asperger. Foram avaliados 103 portadores de TEA não sindrômicos e 18 sindrômicos, sendo as taxas de detecção de alterações potencialmente patogênicas, respectivamente, de 11,6% e 38,9%. Dentre as alterações detectadas 44,4% são menores do que 10 Kbp. Portanto, a estratégia de usar uma lâmina customizada, com alta densidade de sondas complementares aos exons e regiões não codificantes de genes potencialmente envolvidos na etiologia dos TEA, capaz de detectar tanto alterações grandes quanto pequenas, parece ser relevante na tentativa de elucidar o maior número de casos possíveis e melhor compreender esses transtornos. Além disso, essa lâmina também pode ser utilizada como uma ferramenta para auxiliar o diagnóstico clínico e o aconselhamento genético com um custo mais acessível em comparação a outras comerciais ou ao sequenciamento de última geração. Cerca de 33,3% das CNVs observadas afetam região UTR, sugerindo que mutações nessas regiões podem explicar uma proporção significativa dos casos nos quais não são detectadas alterações através de outros testes genômicos, visto que a maioria desses ainda não exploram adequadamente regiões não codificantes. Entre os pacientes autistas não sindrômicos verificou-se que a maioria dos genes afetados por CNVs estão envolvidos em duas principais funções biológicas - sinapses glutamatérgicas e orientação axonal, sugerindo que TEA não sindrômico pode ser causado por disfunção em genes diferentes envolvidos em processos fisiológicos comuns. Diferente do que observamos entre pacientes não sindrômicos, detectamos mais de uma alteração em um mesmo indivíduo ou alterações que englobam mais de um gene entre os pacientes sindrômicos, reforçando o modelo oligogênico para alguns casos de TEA. Por fim, os dados obtidos no estudo da família com portadores de síndrome de Asperger e transtorno autista sugere que a gravidade do quadro clínico possa estar relacionada ao número de mutações e possivelmente por duas mutações diferentes em ambos os alelos de um mesmo gene. Nossos resultados, além de apoiar o envolvimento dos genes MDGA2, FHIT, HTR2A, SHANK2, GRIA3, ZNF778, PRKCα, CDH15, DIAPH3, GCH1, GRM5, MARK1, SLC17A6, IMMP2L, BZRAP1, SYNGAP1, ANK3, MAP1A, GABRR2 e LAMC3 nos TEA também sugere novos genes candidatos: LRRC7, LRRIQ3, CADPS1, NUFIP, SEMA3A, SNAP29, MBD2, GAD2, DGKH e PARD3 / The autism spectrum disorders (ASD) are neuropsychiatric conditions typically characterized by social deficits, communication difficulties, stereotyped or repetitive behaviors and interests. Several studies have shown that these disorders have a complex and heterogeneous genetic etiology, which makes difficult to identify the causal factors. Approximately 70% of cases are idiopathic. In order to identify etiological mechanisms associated with ASD, we have used the following strategies: customized a microarray CGH platform that allows detection not only of large CNVs, but also alterations smaller than 10 kbp in exons and UTR regions of potential candidate genes, the comparison between the types of rearrangements detected in syndromic and non-syndromic patients and further, more detailed investigation of a family segregating both autistic disorder and Asperger syndrome. We evaluated 103 nonsyndromic and 18 syndromic patients by the custom-designed array and the detection rate of possibly pathogenic alterations were, respectively, 11.6% and 38.9%. Among these CNVs, 44.4% are smaller than 10 kbp. Therefore, the strategy of using a custom-designed array, enriched with probes targeted to genes potentially involved in the ASD etiology and able to detect both large and small CNVs, seems to be relevant in an attempt to elucidate the largest number of cases and to better understand these disorders. Furthermore, this platform can also be used as a tool to support the clinical diagnosis and genetic counseling with a more affordable cost compared to conventional other or next-generation sequencing. Approximately 33.3% of the observed CNVs affect UTR region, suggesting that mutations in non-coding regions might explain a significant proportion of ASD cases negative for most genomic screenings, which still do not explore adequately these regions. Among nonsyndromic autistic patients we found that most of the genes affected by CNVs are involved in two main biological functions - glutamatergic synapses and axonal guidance, suggesting that nonsyndromic ASD can be caused by dysfunction in different genes of a few common physiological processes. In contrast to our findings in nonsyndromic patients, we detected more than one alteration in a single individual or alterations that involve more than one gene among the syndromic patients, reinforcing the oligogenic model for some cases of ASD. Finally, the data obtained in the study of the family segregating both Asperger syndrome and autistic disorder suggests that the severity of ASD seems to be modulated by the number of hits and possibly by hits in both alleles of the same gene. Our results support the involvement of genes MDGA2, FHIT, HTR2A, SHANK2, GRIA3, ZNF778, PRKCα, CDH15, DIAPH3, GCH1, GRM5, MARK1, SLC17A6, IMMP2L, BZRAP1, SYNGAP1, ANK3, MAP1A, GABRR2 and LAMC3 in ASD etiology and also suggests new candidates: LRRC7, LRRIQ3, CADPS1, NUFIP, SEMA3A, SNAP29, MBD2, GAD2, DGKH and PARD3

Atualmente a procura por produtos sustentáveis têm-se mostrado cada vez mais frequente e promissora. Em espécies de importância comercial, procura-se obter a maior produtividade possível dentro de um curto espaço de tempo aliado à preservação do meio ambiente. Dentro disso, a transformação genética de plantas se mostra uma alternativa atrativa para a geração de variedades de cana-de-açúcar que gerem produtos de maneira mais eficaz. O sucesso da transformação genética está diretamente associada a cultura de tecidos de plantas que precisa ser adequada a cada genótipo e situação de cultivo, sendo a luminosidade um dos principais fatores para a produção de plantas vigorosas. Outro fator importante é a seleção das plantas transgênicas, que precisam ser submetidas a uma quantidade de agente seletivo suficiente para identificar as plantas modificadas geneticamente. Em cana-de-açúcar, a identificação de plantas transgênicas por PCR e a definição do número de cópias é um procedimento de difícil execução e muito oneroso. Isto se dá pois no processo transformação via biolística, a inserção de genes é aleatória, produzindo plantas com variados números de cópias. Em consideração a estes fatores envolvidos na eficiência de obtenção de plantas transgênicas de cana-de-açúcar, os objetivos deste trabalho foram o aperfeiçoamento do protocolo de cultura de tecidos, transformação genética da variedade SP803280 com os genes xth, AtDdm1, como também, definir genes de referência para a quantificação do número de cópias dos genes xth e AtDdm1 inseridos na variedade SP803280 e do gene neo na RB835089, análise de ploidia e tamanho de genoma dos eventos transgênicos comparado com as plantas controle. No estudo a respeito da melhor qualidade de luz durante o cultivo in vitro na fase de regeneração de plantas, tem-se que a luz branca e a junção das luzes LED e branca se mostraram melhores para regeneração e desenvolvimento das plantas enquanto que para plântulas, as luzes LED e branca separadamente foram mais efetivas no crescimento. Para a seleção das plantas uma concentração de geneticina entre 40 e 50 mgL-1 é recomendada. As taxas de sucesso nas transformações genéticas para o gene xth variaram entre 2,5 a 18,3% dependendo do experimento e para AtDdm1 foi de 2,2% em um bombardeamento.Não houveram alterações de ploidia e tamanho do genoma nos transgênicos das duas variedades em relação à planta selvagem. Os genes p4h e prr foram identificados como os melhores para a quantificação relativa de genes inseridos por PCR em tempo real na variedade SP803280 enquanto que para a RB835089 aprt e prr se mostraram mais eficazes. A análise do número de cópias inseridas em eventos transgênicos por PCR em tempo real foi possível através das duas metodologias de cálculo testados por este trabalho, com resultados que concordam com uma tendência nesta determinação de maneira simples e rápida. / Currently the demand for sustainable products has been shown to be frequent and promising. In species of commercial importance, there is an effort to obtain the highest possible productivity in a short time, along with the environment preservation. In this context, genetic transformation of plants appears as an attractive alternative for the development of sugarcane varieties able to generate products in a more effective way. The genetic transformation success is directly associated to plant tissue culture that requires specific condition for each genotype and cultivation process, in which, luminosity is one of the main factors that determines the production of vigorous plants. Another important factor is the selection of transgenic plants, that occur by exposing plants to a sufficient amount of selective agent in order to identify only genetic modified plants. In sugarcane, identification of transgenic plants by PCR and the definition of copy numbers is a difficult procedure to implement and usually is very costly. It is because in the process of genetic transformation by biolistic, the insertion of genes occurs randomly and also produce plants with varied copy numbers. In consideration of these factors directly involved in the efficiency to obtain sugarcane transgenic plants the objectives of this study were the improvement of a tissue culture protocol, the genetic transformation of the variety SP803280 with xth and AtDdm1 genes. Also, the studies include the definition of reference genes for determining the number of copies inserted of xth and AtDdm1 genes into the variety SP803280 and neo gene in RB835089, ploidy analysis and genome size of the transgenic events compared to control plants. In the study related to the best light quality for in vitro plant regeneration, white light and the combination of LED and white lights proved to be better for plants regeneration and development while for seedlings, LED and white light separately were more effective for growth. In order to obtain selection of transgenic plants, geneticin concentration between 40 and 50 mg L-1 is recommended. Success rates in xth genetic transformation ranged from 2.5 to 18.3% depending on the experiment, and for AtDdm1 was only 2.2% in just one biolistic bombardment. There were no changes in ploidy and genome size in transgenic events related to their wild type plant. The genes p4h and prr were defined to be the best for determining the copy number of transgenic events by real time PCR in SP803280 variety, while for RB835089, the genes aprt and prr were the most effective. The analysis of the number of inserted copies was possible using the two calculation methodologies tested by this work, with results that agree with a tendency in a simple and fast quantification methodology.

Cancer related mortality is almost always due to metastatic dissemination of the primary disease. While research into the biological mechanisms that drive the metastatic cascade continues to unravel its molecular underpinnings, progress in our understanding of biological phenomena such as tumour heterogeneity and its relevance to the origins of distant recurrence or the emergence of resistance to therapy has been limited.In parallel to major breakthroughs in the development of high throughput molecular techniques, researchers have begun to utilise next generation sequencing to explore the relationship between primary and matched metastatic tumours in diverse types of neoplasia. Despite small cohort sizes and often, a limited number of matched metastases for each patient, pioneering studies have uncovered hitherto unknown biological processes such as the occurrence of organ specific metastatic lineages, polyclonal seeding and homing of metastatic cells to the primary tumour bed. While yet other studies continue to highlight the potential of genomic analyses, at the time this thesis was started, an in-depth knowledge of disease progression and metastatic dissemination was currently lacking in breast cancers.Herein, we employed phylogenetic inference methods to investigate intra-tumour heterogeneity and evolution of breast cancers. A combination of whole exome sequencing, custom ultra-deep resequencing and copy number profiling were applied to primary tumours and their associated metastases from ten autopsied breast cancer patients. Two modes of metastatic progression were observed. In the majority of cases, all distant metastases clustered on a branch separate from their primary lesion. Clonal frequency analysis of somatic mutations showed that the metastases had a monoclonal origin and descended from a common metastatic precursor. Alternatively, the primary tumour was clustered alongside metastases with early branches leading to distant organs. This dichotomy coincided with the clinical history of the patients whereby multiple seeding events from the primary tumour alongside cascading metastasis-to-metastasis disseminations occurred in treatment naïve de novo metastatic patients, whereas descent from a common metastatic precursor was observed in patients who underwent primary surgery followed by systemic treatment. The data also showed that a distant metastasis can be horizontally cross-seeded and finally revealed a correlation between the extent of somatic point mutations private to the distant lesions and patient overall survival. In an unrelated dataset of relapsed breast cancer patients with matched primary and distant lesions profiled using whole genome sequencing, the landscape of somatic alterations confirmed the time dependency of copy number aberrations implying that cancer phylogenies can be dated using a molecular clock.The work presented here harnesses the strength of high throughput genomic techniques and state of the art phylogenetic tools to tell the evolutionary history of breast cancers. Our results show that the linear and parallel models of metastatic dissemination which have been held as near doctrines for many years are overstated point of views of cancer progression. Beyond the biological insights, these results suggest that surgical excision of the primary tumour in de novo metastatic breast cancers might reduce dissemination in selected cases hence providing a potential biological rationale for this practice. Similarly, there is no strong evidence of benefit in overall survival from surgical resection of oligo-metastases in breast cancer. From our analyses, metastatic lesions constitute an additional source of seeding and heterogeneity in advanced breast cancer. The data presented here is too small to derive practice-changing evidence, but supports the concept that resecting isolated metastases may be of clinical benefit in oligo-metastatic breast cancer patients. In both cases, results from larger prospective studies are warranted. / Doctorat en Sciences biomédicales et pharmaceutiques (Médecine) / info:eu-repo/semantics/nonPublished

Les variations du nombre de copies (CNVs) incluent les délétions et les duplications de régions chromosomiques d’une taille variant de 50 pb à plusieurs Mb. Depuis 2005, les études d’association pangénomiques (GWAS) ont permis d’associer certains larges CNVs à des maladies syndromiques associées à la déficience intellectuelle incluant les syndromes de DiGeorge, Williams, Angelman, etc. En fonction de la densité génique de la région d’intérêt et de la variabilité des phénotypes associés, l’étude de la physiopathologie des syndromes peut être extrêmement complexe. La modélisation murine offre de nombreux avantages pour l’identification des gènes candidats et la compréhension des mécanismes moléculaires associés à ces pathologies.Les travaux présentés dans ce manuscrit consistent en la caractérisation des modèles murins pour cinq maladies syndromiques associées aux CNVs : la monosomie 21 partielle ainsi que les réarrangements des régions 16p11.1 et 17q21.31. Les caractérisations anatomiques, métaboliques et comportementales des animaux nous ont permis d’évaluer un grand nombre de paramètres associés à la symptomatique humaine. Nous avons également réalisé des analyses électrophysiologiques et transcriptomiques en ciblant nos investigations sur l’hippocampe, structure cérébrale qui joue un rôle central dans les processus de mémoire et d’apprentissage. Ce projet de recherche s’inscrit dans une perspective plus large qui est l’identification des gènes candidats pour les phénotypes observés et le développement de premières stratégies thérapeutiques pouvant potentiellement aboutir à l’amélioration des capacités cognitives des patients. / Copy number variations (CNVs) include deletions and duplications of chromosomal regions ranging in size from 50bp to several Mb. Since 2005, genome-wide association studies (GWAS) have associated some large CNVs to syndromic diseases linked to intellectual disability including DiGeorge, Williams, Angelman syndroms, etc. Depending on the gene density of the region of interest and the variability of symptoms, the study of the pathophysiology of syndromes can be extremely complex. Mouse modeling show many advantages for the identification of candidate genes and the understanding of molecular mechanisms associated with these diseases.The work presented in this manuscript consists of the characterization of mouse models of five syndromic diseases associated with CNVs: partial monosomy 21 and rearrangements of 16p11.2 and 17q21.31 regions. Anatomical, metabolic and behavioral characterizations of animals allowed us to evaluate a broad number of parameters associated with human phenotypes. We also performed electrophysiological and transcriptomic analysis focusing our investigation on the hippocampus which has a major role in learning and memory processes. This project is part of a wider perspective which is the identification of candidate genes for the different phenotypes we observe in the mouse and the development of first treatment strategies which can potentially lead to the improvement of cognitive capacity of patients.

Brain disorders present a significant burden on affected individuals, their families and society at large. Existing diagnostic tests suffer from a lack of genetic biomarkers, particularly for substance use disorders, such as alcohol dependence (AD). Numerous studies have demonstrated that AD has a genetic heritability of 40-60%. The existing genetics literature of AD has primarily focused on linkage analyses in small family cohorts and more recently on genome-wide association analyses (GWAS) in large case-control cohorts, fueled by rapid advances in next generation sequencing (NGS). Numerous AD-associated genomic variations are present at a common frequency in the general population, making these variants of public health significance. However, known AD-associated variants explain only a fraction of the expected heritability. In this dissertation, we demonstrate that systems biology applications that integrate evolutionary genomics, rare variants and structural variation can dissect the genetic architecture of AD and elucidate its heritability. We identified several complex human diseases, including AD and other brain disorders, as potential targets of natural selection forces in diverse world populations. Further evidence of natural selection forces affecting AD was revealed when we identified an association between eye color, a trait under strong selection, and AD. These findings provide strong support for conducting GWAS on brain disorder phenotypes. However, with the ever-increasing abundance of rare genomic variants and large cohorts of multi-ethnic samples, population stratification becomes a serious confounding factor for GWAS. To address this problem, we designed a novel approach to identify ancestry informative single nucleotide polymorphisms (SNPs) for population stratification adjustment in association analyses. Furthermore, to leverage untyped variants from genotyping arrays – particularly rare variants – for GWAS and meta-analysis through rapid imputation, we designed a tool that converts genotype definitions across various array platforms. To further elucidate the genetic heritability of brain disorders, we designed approaches aimed at identifying Copy Number Variations (CNVs) and viral insertions into the human genome. We conducted the first CNV-based whole genome meta-analysis for AD. We also designed an integrated approach to estimate the sensitivity of NGS-based methods of viral insertion detection. For the first time in the literature, we identified herpesvirus in NGS data from an Alzheimer’s disease brain sample. The work in this dissertation represents a three-faceted advance in our understanding of brain disease etiology: 1) evolutionary genomic insights, 2) novel resources and tools to leverage rare variants, and 3) the discovery of disease-associated structural genomic aberrations. Our findings have broad implications on the genetics of complex human disease and hold promise for delivering clinically useful knowledge and resources.

Orientadores: Antonia Paula Marques de Faria, Maricilda Palandi de Mello / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-30T05:34:46Z (GMT). No. of bitstreams: 1 Henrique_PamelaPontes_M.pdf: 8320960 bytes, checksum: 1d8ff3e1253bf81cc18b4afd51572860 (MD5) Previous issue date: 2015 / Resumo: A deficiência intelectual ligada ao X (DILX) é uma das causas genéticas mais frequentes de deficiência intelectual (DI), ocorrendo em 10 a 12% de todos os homens afetados, provavelmente pelo maior número de genes identificados no cromossomo X em comparação a qualquer segmento autossômico. Cerca de 100 genes seriam determinantes de DILX, porém mesmo com o conhecimento do papel de vários deles, há aspectos a serem elucidados, como a contribuição de cada um na determinação da DI ou ainda as correlações genótipo-fenótipo, cuja análise depende da investigação genética em indivíduos com DI idiopática. Entre os métodos que permitem a investigação molecular dessa condição destaca-se a Multiplex Ligation-dependent Probe Amplification (MLPA) por sua rapidez, sensibilidade e baixo custo. O objetivo do presente estudo foi investigar alterações em genes do cromossomo X pela técnica de MLPA em pacientes do sexo masculino com atraso global do desenvolvimento ou DI de origem indeterminada. Foram investigados 107 indivíduos com o kit SALSA MLPA P106 MRX probemix (MRC-Holland), 104 deles apresentaram resultado na faixa de normalidade e em três foram identificadas alterações do número de cópias interpretadas como duplicações. O paciente P13 apresentou alteração no gene HUWE1, que atua no controle da diferenciação neural e tem mutações descritas em algumas famílias com DI de moderada a grave; no paciente P139 foram identificadas alterações nos genes SCL6A8 e GDI, ambas confirmadas pela análise por Real Time Polymerase Chain Reaction (qPCR); mutações no primeiro são incluídas entre as síndromes de deficiência de creatina, com fenótipos variando de DI leve e atraso de fala até DI grave, convulsões e alterações de comportamento no sexo masculino, enquanto no segundo se associam à DILX inespecífica; já no paciente P39 foi detectada alteração no gene ARX, relacionado a mais de uma condição classificada como DILX sindrômica, que não foi confirmada. Como apenas alguns éxons relacionados à DILX foram investigados, não se afasta a eventual ocorrência de rearranjos localizados em regiões não abordadas pelo kit utilizado. Contudo, a técnica utilizada se mostrou uma opção de custo relativamente baixo e fácil reprodutibilidade, sendo viável para aplicação em algoritmos de investigação da DI. Os resultados reforçam a relevância da DILX entre as causas de DI, justificando a inclusão de testes moleculares específicos para a elucidação diagnóstica dessa condição / Abstract: X-linked intellectual disability (XLID) is one of the most frequent genetic causes of intellectual disability (ID), occurring in 10-12% of all affected men, probably because the larger number of identified genes on the X chromosome related to this condition than in any other autosomal segment. Although about 100 genes have been considered as determinant of XLID, the the role of several of these genes remains yet be elucidated despite the knowledge on the function of several of them. For instance, the contribution of each gene in determining the ID and the genotype-phenotype correlation depend on the genetic investigation of affected individuals. The Multiplex Ligation-dependent Probe Amplification (MLPA) is among the methods that allow molecular investigation of this condition because it is rapid and low cost and presents high sensitivity. The aim of this study was to investigate copy number variations in X-linked genes by MLPA technique in males with global developmental delay or ID of undetermined origin. A hundred and seven individuals were investigated using SALSA MLPA P106 MRX kit (MRC-Holland) and alterations were confirmed by Real Time Polymerase Chain Reaction (qPCR). A normal invariant pattern was observed in 104 out of 107 individuals, and three showed variations that have been interpreted as duplications. Patient P13 showed increased signal for HUWE1 gene, which plays a role in the control of neural differentiation. HUWE1 mutations have been described in families with moderate or severe ID. Patient P139 showed increased signals corresponding to regions of SCL6A8 and GDI1 genes. The former is included among genes involved in the creatine deficiency syndrome whose phenotype can range from mild ID and speech delay to severe ID, convulsions and behavior changes in males, and the latter is involved with non-syndromic XLID. Conversely, the variation in ARX gene, which is associated to more than one condition classified as syndromic XLID, observed in MLPA analysis for patient P39 was not confirmed in the qPCR assay. As only a few exons related to XLID were investigated, it does not rule out the possible occurrence of rearrangements located in regions not covered by the kit used. However, the technique employed was an easily reproducible, relatively low cost option, manageable for application in ID research algorithms. The results reinforce the importance of XLID among the causes of ID, justifying the inclusion of specific molecular tests for the laboratory diagnosis of this condition / Mestrado / Ciencias Biomedicas / Mestra em Ciências Médicas

O transtorno do espectro autista (ASD) é uma doença clinica e geneticamente heterogênea, com mecanismo etiológico ainda pouco conhecido. Assim, os principais objetivos deste trabalho foram descrever as características clínicas e genéticas de pacientes brasileiros com ASD, bem como determinar o risco de recorrência e a herdabilidade. Verificamos que a maioria das comorbidades avaliadas tem prevalência similar àquelas anteriormente descritas. A hipotonia exibiu maior prevalência no sexo feminino. A ausência de fala apresentou prevalência significativamente maior no grupo de pacientes com comorbidades, sendo que a gravidade da fala foi positivamente correlacionada com a presença das crises convulsivas. A herdabilidade estimada foi de 76% e o risco de recorrência ~5%. As alterações citogenéticas e os casos positivos para a Síndrome do X-Frágil explicaram cerca de 8% dos casos de ASD da nossa amostra. As CNVs nas regiões estudadas foram detectadas em 2,7% da amostra. Nós verificamos que há penetrância incompleta do ASD para as regiões. O estudo mais detalhado dos dois casos de duplicação da região 15q13.3, envolvendo somente o gene CHRNA7, mostrou que um dos pacientes (F5240) exibiu uma segunda CNV, possivelmente patogênica. A análise in silico sugeriu que genes que interagem diretamente com o CHRNA7 podem conter mutações patogênicas e, juntamente com a duplicação do 15q13.3, possivelmente estão envolvidos na etiologia do ASD. Este estudo mostrou que é necessário fazer uma ampla caracterização genética dos pacientes, para possibilitar o estudo dos possíveis mecanismos moleculares envolvidos na causa do ASD / Autism Spectrum Disorder (ASD) is a clinically and genetically heterogeneous disease and its etiological mechanisms are still poorly understood. The main objectives of this study were to describe the clinical and genetic features of Brazilian patients with ASD, and to determine the recurrence risk and heritability. Great part of the comorbidities assessed here had comparable prevalence to those of previous works. The hypotonia was significantly prevalent in the female sex. Absent speech was significantly more frequent in patients with comorbidities, and severity of speech problems was positively correlated with presence of seizures. Heritability was estimated as 76% and the recurrence risk as approximately 5%. Cytogenetic alterations and positive results for Fragile X Syndrome explain about 8% of the ASD etiology of our sample. The CNVs at the chromosomal regions 15q11-q13, 16p11.2 and 22q13 were present in 2.7% of the sample. Incomplete penetrance of ASD was observed for the 16p and 15q regions. Further investigation of the two cases with duplication of the region 15q13.3, involving only the CHRNA7 gene, revealed that one of them (F5240) exhibited a second possible pathogenic CNV. In silico analysis suggested that genes interacting directly with the CHRNA7 could harbor pathogenic mutations and, together with the duplication at 15q13.3, could be involved in the ASD etiology. This study showed the necessity of a broad genetic characterization of patients with ASD, to enable the elucidation of possible molecular mechanisms related to ASD etiology

Introduction. Sperm parameter analysis is the standard method of male fecundity testing; however, minimal evidence supports associations between individual sperm parameters and reproductive outcomes. Our previous work shows strong associations between sperm mitochondrial DNA copy number (mtDNAcn) and time-to-pregnancy (TTP) in general populations, and between mtDNAcn and fertilization outcomes in clinical populations. Thus it is possible for sperm mtDNA biomarkers to act as summary measures of semen quality. In this study, we developed a sperm quality index (SQI) from semen parameters and compared its ability to measure fecundity to sperm mtDNAcn. Methods. We received 384 semen samples from the Longitudinal Investigation of Fertility in the Environment Study. Sperm mtDNAcn and mtDNA deletions (mtDNAdel) were quantified using a triplex probe-based qPCR method. The SQI was developed by ranking and summing select sperm parameters within the study population, including sperm concentration, sperm count, normal morphology, high DNA stainability, and DNA fragmentation to create a cumulative index. Discrete-time proportional hazards models were used to determine fecundability odds ratios (FOR), indicating associations between mtDNAcn, SQI, and TTP. Receiver operating characteristic (ROC) analyses determined the validity of the SQI and mtDNAcn as predictors of pregnancy within 12 months. Results. The SQI was highly associated with mtDNAcn, both continuously (Spearman Rho: -0.487; p-value: <0.001) and in deciles (ANOVA p-value: <0.001). The SQI (FOR: 1.25; 95% confidence interval (CI): 1.09, 1.43) and mtDNAcn (FOR: 0.754; 95% CI: 0.657, 0.866) performed similarly in discrete-time survival models and indicated a significant decrease and increase in TTP, respectively. MtDNAcn more effectively predicted pregnancy within 12 months (AUC: 0.703; 95% CI: 0.617, 0.789) than the SQI (AUC: 0.642; 95% CI: 0.531, 0.753). With multiple predictors, mtDNAcn outperformed summary models, with addition of the SQI and percent normal morphology minimally increasing model efficacy (AUC: 0.718, 95% CI: 0.617, 0.819). Conclusion. The association between the SQI and mtDNAcn suggest that mtDNAcn may serve as a summary biomarker for overall sperm quality. Neither individual nor summed sperm parameters are useful indicators of couple fecundity and reproductive outcomes compared to mtDNAcn. These results suggest that mtDNAcn has potential for use as a biomarker of fecundity.

Mental retardation (MR) is a very heterogeneous common neurodevelopmental disorder with a population prevalence of 2.5-3 %. The importance of genetic factors in the development of MR is high but in a significant number of cases the etiology remains unexplained. Recent studies using array methods pointed to frequent occurrence of copy number variants (CNVs) in patients with MR. Pathogenic CNVs were identified in 10-15 % patients with idiopathic MR and normal karyotype. The aim of our work was the analysis of genome-wide gains and losses of genetic material in a group of Czech patients with MR and a thorough bioinformatic analysis of the genetic changes identified aiming at the assessment of their clinical significance. We performed whole genome analysis using the HumanCytoSNP-12 BeadChips (Illumina) in 183 patients with idiopathic MR, normal karyotype and no FMR1 gene expansion. Data analysis was carried out using two independent programmes, GenomeStudio and QuantiSNP. The findings were subjected to two rounds of thorough bioinformatic analysis. Based on this analysis we classified the CNVs into 4 categories: pathogenic CNVs, probably pathogenic CNVs, CNVs with uncertain clinical significance and benign CNVs. With the exception of the benign variants, all CNVs were confirmed using an independent laboratory...

In this thesis, I investigate the genetics of neuropsychiatric disorders by analysing large data sets derived from high-throughput experiments, using novel comparative genomics approaches. In the first project, I explore characteristics of rare, de novo copy number variants identified among autism patients by employing various bioinformatics resources including Mouse Genome Informatics phenotypes, Gene Ontology terms, and protein-protein interactions. I describe how I objectively identified a number of mouse model phenotypes that are significantly associated with autism, and that provide insight into the aetiologies for both copy number deletions and duplications. In the second project, I investigate the genetics of obsessive-compulsive disorder by resequencing genomic regions of human case-control cohorts and the best spontaneous disease model organisms, namely dogs with canine compulsive disorder, and breed-matched controls. Targeted sequencing experiments yielded a large number of high-quality genetic variants in both humans and dogs. I prioritised variants and genes using case- control comparisons and functional annotations such as types of mutation, evolutionary conservation status and regulatory marks. In turn, I generated several hypotheses that are experimentally tractable. Replication of these findings in a larger cohort is necessary, although it lies beyond the scope of this thesis. Results from both projects indicate that the analytical frameworks employed in this thesis could be profitably applied to other neuropsychiatric disorders.