High-throughput genomic datasets obtained from microarray or sequencing studies have revolutionized the field of molecular biology over the last decade. The complexity of these new technologies also poses new challenges to statisticians to separate biological relevant information from technical noise. Two methods are introduced that address important issues with normalization of array comparative genomic hybridization (aCGH) microarrays and the analysis of RNA sequencing (RNA-Seq) studies. Many studies investigating copy number aberrations at the DNA level for cancer and genetic studies use comparative genomic hybridization (CGH) on oligo arrays. However, aCGH data often suffer from low signal to noise ratios resulting in poor resolution of fine features. Bilke et al. showed that the commonly used running average noise reduction strategy performs poorly when errors are dominated by systematic components. A method called pcaCGH is proposed that significantly reduces noise using a non-parametric regression on technical covariates of probes to estimate systematic bias. Then a robust principal components analysis (PCA) estimates any remaining systematic bias not explained by technical covariates used in the preceding regression. The proposed algorithm is demonstrated on two CGH datasets measuring the NCI-60 cell lines utilizing NimbleGen and Agilent microarrays. The method achieves a nominal error variance reduction of 60%-65% as well as an 2-fold increase in signal to noise ratio on average, resulting in more detailed copy number estimates. Furthermore, correlations of signal intensity ratios of NimbleGen and Agilent arrays are increased by 40% on average, indicating a significant improvement in agreement between the technologies. A second algorithm called gamSeq is introduced to test for differential gene expression in RNA sequencing studies. Limitations of existing methods are outlined and the proposed algorithm is compared to these existing algorithms. Simulation studies and real data are used to show that gamSeq improves upon existing methods with regards to type I error control while maintaining similar or better power for a range of sample sizes for RNA-Seq studies. Furthermore, the proposed method is applied to detect differential 3' UTR usage.

Submitted by Cleide Dantas (cleidedantas@ufpa.br) on 2014-06-27T14:12:22Z No. of bitstreams: 2 license_rdf: 23898 bytes, checksum: e363e809996cf46ada20da1accfcd9c7 (MD5) Dissertacao_CaracterizacaoGenomaTumores.pdf: 2749832 bytes, checksum: e6649779ee4f854ea903101a84af2063 (MD5) / Approved for entry into archive by Ana Rosa Silva (arosa@ufpa.br) on 2014-07-31T12:53:36Z (GMT) No. of bitstreams: 2 license_rdf: 23898 bytes, checksum: e363e809996cf46ada20da1accfcd9c7 (MD5) Dissertacao_CaracterizacaoGenomaTumores.pdf: 2749832 bytes, checksum: e6649779ee4f854ea903101a84af2063 (MD5) / Made available in DSpace on 2014-07-31T12:53:36Z (GMT). No. of bitstreams: 2 license_rdf: 23898 bytes, checksum: e363e809996cf46ada20da1accfcd9c7 (MD5) Dissertacao_CaracterizacaoGenomaTumores.pdf: 2749832 bytes, checksum: e6649779ee4f854ea903101a84af2063 (MD5) Previous issue date: 2014 / Os tumores bem diferenciados da tireóide representam mais de 95% das neoplasias malignas da glândula. A identificação pré-operatória dos carcinomas papilíferos está bem estabelecida através dos métodos de Punção aspirativa por Agulha fina e Ultrassonografia, com quase 100% de acurácia, enquanto os tumores foliculares significam um dilema para o cirurgião, visto que os métodos existentes não conseguem determinar com eficiência o diagnóstico sendo que 60-80% dos casos operados são benignos. Dessa forma, com o intuito de se analisar alterações genômicas do tipo variações no número de cópias (CNVs) que possam diferenciar esse tumor de outros tipos de doenças da tireóide, foram analisados 13 pacientes com doença tireoidiana (3 bócios, 2 hiperplasias, 4 adenomas foliculares e 4 carcinomas foliculares ) mais 1 individuo sadio através do método de aCGH, para identificação de CNVs que pudessem determinar com eficiência a presença de carcinoma folicular. Os achados foram confrontados com dados de carcinomas papilífero clássico (4 pacientes) e variante folicular (2 pacientes). Foram encontradas 725 CNVs na amostra, 703 dos pacientes com patologia. Dentre estas foram selecionadas 18 regiões mais frequentes. Houve um padrão de amplificação maior em pacientes jovens com adenomas e deleção em pacientes mais velhos. Os pacientes com carcinoma apresentaram taxas de CNVs muito próximas. Os carcinomas foliculares apresentaram padrões exclusivos de alteração nos cromossomos 8 e 12. Concluímos, assim, que os carcinomas foliculares da tireoide são uma patologia com um padrão exclusivo de alterações, não havendo correlação de progressão tumoral a partir de adenomas foliculares, sendo que duas regiões -8p22 e 12p13.32-p13.33, estão presentes em 100% e 75% das amostras respectivamente, podendo ser fortes candidatos a marcadores desse tipo tumoral. / More than 95% of thyroid gland malignancies are well-differentiated tumors. Preoperative diagnosis accuracy for papillary carcinomas, based on FNAC (Fine Needle Aspiration Cytology) and ultrasound screenings, has become nearly 100%. Nevertheless, when follicular neoplasm diagnosis is concerned, this reality is quite different. Using current preoperative screening tools, 60 – 80% of patients suspected to present follicular thyroid cancer, when operated turn out to suffer from benign disease. Therefore, in an effort to improve these results, genomic analysis of Copy Number Variations (CNV) that may more precisely differentiate follicular tumor from other thyroid conditions were carried out in 13 patients (3 bearing goiters, 2 hyperplasias, 4 follicular adenomas, 4 follicular carcinomas, 1 healthy individual). CNVs were tracked through aCGH method in order to detect follicular carcinoma most accurately. Results were compared with classic papillary carcinoma (4 subjects) and follicular variant (2 subjects). Samples demonstrated 725 CNVs, 703 of which belonging to patients with disease. Among these, 18 most frequent regions were selected. Patterns of amplification were more frequent in younger patients, while deletions were more frequent in the elder ones. Carcinoma patients presented very close CNV rates. Also, exclusive patterns of chromosomes 8 and 12 alterations were noticed in follicular carcinoma. Thus, it is possible to conclude that thyroid follicular carcinoma is a condition comprehending exclusive patterns of alterations, and progression of this disease is not related to follicular adenomas. Finally, regions -8p22 and 12p13.32-p12.33 were detected in 100% and 75% of samples respectively, therefore, may be deemed as possible tumoral markers.

Submitted by Cássio da Cruz Nogueira (cassionogueirakk@gmail.com) on 2017-08-30T12:00:55Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_AlteracoesGenomicasQuantitativas.pdf: 6280298 bytes, checksum: b16a105099c01920d2f9f9a43d028192 (MD5) / Approved for entry into archive by Irvana Coutinho (irvana@ufpa.br) on 2017-08-30T14:59:52Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_AlteracoesGenomicasQuantitativas.pdf: 6280298 bytes, checksum: b16a105099c01920d2f9f9a43d028192 (MD5) / Made available in DSpace on 2017-08-30T14:59:52Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_AlteracoesGenomicasQuantitativas.pdf: 6280298 bytes, checksum: b16a105099c01920d2f9f9a43d028192 (MD5) Previous issue date: 2016-05-31 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico / O câncer gástrico é o quinto tipo tumoral mais frequente e a terceira maior causa de morte por câncer no mundo. A despeito do progresso no tratamento do câncer gástrico avançado, o prognóstico do paciente permanece muito ruim, principalmente em decorrência do diagnóstico tardio. Esse paradigma implica a necessidade de pesquisar e identificar biomarcadores moleculares para o diagnóstico precoce, bem como para o monitoramento da doença, contribuindo ainda para o desenenvolvimento de novas abordagens terapêuticas. Desta forma, o presente estudo objetivou investigar alterações no número de cópias de DNA no adenocarcnoma gástrico através da técnica de Hibridização Genômica Comparativa em array (aCGH) e selecionar genes para a validação em um maior número de amostras, utilizando PCR em tempo real, no intuito de encontrar potenciais biomarcadores moleculares para esse tipo tumoral. Através dos resultados do aCGH, foram identificadas 22 alterações nunca correlacionadas com a carcinogênese gástrica, bem como diversas alterações associadas significativamente com o extravasamento da serosa e com pacientes com idade igual ou inferior a 50 anos. Levando em consideração que a maioria dos genes observados alterados nunca foram descritos como envolvidos no processo de carcinogênese gástrica, foram selecionados para validação genes cujas alterações apresentaram alguma consistência com trabalhos já publicados na literatura em outros tipos de câncer. Assim, foram investigadas por PCR em tempo real as amplificações dos genes RTEL1, B4GALT5, TRPV2 e ABCA13. Os resultados demonstraram uma frequência elevada de amplificação desses genes, porém as associações estatísticas com os dados clínicopatológicos dos genes TRPV2, com pacientes jovens, e ABCA13, com o extravasamento da serosa, observadas pelo aCGH, não foram confirmadas. Por outro lado, novas associações significativas foram observadas, tais quais a amplificação recorrente do gene RTEL1, que foi associada com idade avançada e com o tipo intestinal do adenocarcinoma gástrico; a amplificação recorrente do gene B4GALT5, que foi associada com o tipo intestinal do adenocarcinoma gástrico; a amplificação recorrente do gene TRPV2, que foi associada com metástase linfonodal; a amplificação recorrente do gene ABCA13, que foi associada com metástase linfonodal e com pacientes do gênero masculino e a co-amplificação dos genes RTEL1 e ABCA13, que foi associada com estadiamento avançado. Desta forma, o aCGH mostrou-se uma ferramenta útil para a investigação de novos genes associados com a carcinogênese. Ademais, a amplificação dos genes RTEL1, B4GALT5, TRPV2 e ABCA13 parecem ter um papel importante no desenvolvimento e na progressão do câncer gástrico, podendo ser considerados potenciais marcadores desta doença. / Gastric cancer is the fifth most frequent type of cancer and the third cause of cancer mortality worldwide. Despite progression in treatment of advanced gastric cancer, the prognosis of patients remains poor, in part due to the low rate of diagnosis during its early stages. This paradigm implies the necessity to search and identify molecular biomarkers for early gastric cancer diagnosis, as well as for disease monitoring, thus contributing to the development of new therapeutic approaches. Therefore, this study aimed at investigating copy number variations in gastric adenocarcnoma through array Comparative Genomic Hybridization (aCGH) technique and selecting genes for validation in a larger sample size by using real-time PCR, in order to find potential molecular biomarkers for this tumor type. The aCGH results demonstrated 22 gene alterations never described before as correlated with gastric carinogenesis, as well as several alterations significantly associated with serosal extravasation and patients aged less than or equal 50 years. Given that most of the genes had never been described in gastric cancer, we selected for validation four gene alterations that showed some consistency with studies published in the literature for other types of cancer. Thus, we investigated by real-time PCR the amplifications of RTEL1, B4GALT5, TRPV2 and ABCA13 genes. The results showed a high frequency of amplification of these genes, but the statistical associations with clinicopathological data of TRPV2 gene with younger patients and ABCA13, with serosal extravasation, observed by aCGH, were not confirmed. Moreover, new significant associations were demonstrated, including RTEL1 recurrent amplification associated with advanced age and intestinal type of gastric adenocarcinoma; B4GALT5 recurrent amplification associated with intestinal type of gastric adenocarcinoma; TRPV2 recurrent amplification associated with lymph node metastasis; ABCA13 recurrent amplification associated with lymph node metastasis and male patients and co-amplification of RTEL1 and ABCA13 associated with advanced staging. Therefore, the aCGH proved to be a useful tool for the investigating new genes associated with carcinogenesis. Additionally, recurrent amplification of RTEL1, B4GALT5, TRPV2 and ABCA13 seem to have an important role in the development and progression of gastric cancer and can be considered as potential biomarkers for this disease.

El descubrimiento de las duplicaciones segmentarias (DS) o Low Copy Repeats (LCRs) ha permitido definir nuevos mecanismos evolutivos mediados, en gran parte, por duplicación génica. Las DS son responsables de reordenamientos que pueden ser submicróscopicos dando lugar a pequeñas pérdidas o ganancias de material genómico. La elucidación sobre su implicación y relación en enfermedades humanas ha generado la necesidad de crear nuevos instrumentos de medida que permitan rastrear el genoma humano a una mayor resolución que la conseguida mediante cariotipo normal. Una de estas nuevas técnicas se denomina matrices aCGH. En esta tesis doctoral se han desarrollado métodos que permiten la optimización de la técnica durante el proceso de fabricación e hibridación y que, a su vez, pueden ser aplicados sobre los métodos actuales de detección de CNVs incrementando su sensibilidad y especificidad. Además se ha realizado una comparación entre plataformas aCGH así como un análisis transcriptómico global de muestras alteradas, tomando como modelo de estudio el síndrome de Williams-Beuren que está caracterizado por una deleción parcial en la banda 7q11.23. A parte de ganancias y pérdidas de fragmentos de material génico, las DSs pueden generar copias de genes que pueden acumular cambios respecto el original (PSVs). Algunos de estas PSVs ya se han identificado como patogénicas por ello es de gran utilidad su estudio.

Myelodysplastic syndrome (MDS) is a clonal disease of hematopoesis resulting from damage to hematopoietic stem cells. The most common chromosomal aberration in patients with MDS is deletion of the long arms of chromosome 5, del(5q). The aim of this study is to analyse unbalanced aberrations of chromosome 5 in MDS patients, to compare the extent of 5q deletion in groups of patients with isolated del(5q) and with del(5q) in complex karyotypes, and to study the effect of the extent of del(5q) on overall survival and prognosis of the disease. We combined cytogenomic methods to examine 88 bone marrow samples from patients with MDS and del(5q) confirmed by conventional banding methods. Del(5q) was present in the karyotype as an isolated aberration in 31 patients (35,2 %), in combination with one other clonal aberration in 9 patients (10,2 %), and as part of complex karyotypes in 48 patients (54,6 %). Patients with complex karyotypes had a lower overall survival than patients with isolated del(5q). The occurrence of complex karyotypes was associated with a large extent of 5q deletion. When both the occurrence of complex karyotypes and the extent of 5q deletion were considered, only karyotype complexity had a significant effect on patients' overall survival. The extent of the deletion does not affect...