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Frater, Eric y Eric Frater. "Optical Alignment with CGH Phase References". Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/621452.
Texto completoPaiva, Greicy Helen Gambarini [UNESP]. "Genes candidatos a marcadores tumorais na progressão do adenocarcinoma de próstata indentificados por análise de HR-CGH e CGH-ARRAY". Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/102718.
Texto completoFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
O câncer de próstata (CaP) é a neoplasia mais comumente diagnosticada entre homens no ocidente. Embora tratamentos efetivos para a doença localizada estejam disponíveis atualmente, não há terapia curativa para tumores metastáticos. Além disso, os marcadores diagnósticos utilizados na clínica não conseguem discriminar totalmente a evolução diferencial da doença. Desta forma, o conhecimento das diferenças biológicas entre tumores primários confinados ao órgão e metástases é essencial para o desenvolvimento de novos marcadores e identificação de alvos terapêuticos. Neste estudo a análise baseada na metodologia de HR-CGH cromossômico foi realizada para identificar alterações de ganhos e perdas genômicas em três grupos de amostras: o grupo I, que compreende amostras pareadas de tumor primário e respectivas metástases (11 casos); o grupo II, constituído de pacientes que apresentaram seguimento clínico favorável por mais de 10 anos (5 casos); e o grupo III, constituído por diferentes biópsias do mesmo paciente (5 pacientes com 2 biópsias cada). As amostras foram microdissecadas (amostras a fresco: a partir de lâminas de referência; em blocos de parafina: a laser) e após a obtenção de DNA foram amplificadas (amostras de arquivo: PCR-SCOMP) ou marcadas por nick-translation para a realização de HR-CGH. Os resultados de HR-CGH foram comparados com os dados obtidos da análise de CGH-array num subgrupo de amostras e revelaram concordâncias significativas. Os resultados obtidos na presente investigação revelaram perdas dos cromossomos 1p, 2, 3q, 4p, 5q, 7, 8, 9q, 10q, 11q, 12q, 14q, 15q, 16q, 17q, 18q, 19, 20q e 22q em 80% dos casos avaliados. Além disso, perdas em 17q11.2-25, por exemplo, foram detectadas exclusivamente nos tumores do grupo I e nas suas metástases, e não nos tumores do grupo II, sugerindo que esta alteração deve ser importante...
Prostate cancer (PCa) is the most commonly diagnosed non-cutaneous malignancy and the second leading cause of cancer mortality in men from Occident. Although effective treatments for the localized disease are available, there is no efficient therapy for metastatic tumors. Additionally, clinical diagnostic markers are not able to completely discriminate the differential evolution of the disease. The knowledge of biological differences between localized primary tumors and metastasis can establish new molecular markers and therapeutic targets. In this study, an analysis based on HR-CGH methodology was performed to identify imbalances genomic in three groups of samples: group I, paired samples of primary tumors and its metastasis (11 cases); group II, patients that exhibited favorable follow-up over 10 years (5 cases); and group III, different biopsies from the same patient (5 patients with 2 biopsies each). The tumor samples were submitted to microdissection procedures (fresh samples: from reference slides; paraffin embedded samples: laser), DNA extracted and amplified (archive sample: PCR-SCOMP) or labeled by nick-translation to HR-CGH. The HRCGH results were compared with data obtained from CGH-array analysis of a subgroup of samples and revealed significant concordances. In the present investigation, there were observed losses on chromosomes 1p, 2, 3q, 4p, 5q, 7, 8, 9q, 10q, 11q, 12q, 14q, 15q, 16q, 17q, 18q, 19, 20q and 22q in 80% of the cases. Losses in 17q11.2-25, for instance, were detected exclusively in tumor from group I and its metastasis, but were not found in tumors from group II, suggesting that this alteration must be important in the progression of the disease. Five genes were selected after the comparison between the HR-CGH and CGH-array data. The tumor suppressor genes ARID1A, MTSS1, NME1 and S100A4 and TOP2A (oncogenes) were evaluated by quantitative real time... (Complete abstract click electronic access below)
Paiva, Greicy Helen Gambarini. "Genes candidatos a marcadores tumorais na progressão do adenocarcinoma de próstata indentificados por análise de HR-CGH e CGH-ARRAY". Botucatu : [s.n.], 2009. http://hdl.handle.net/11449/102718.
Texto completoBanca: Spencer L. M. Payão
Banca: Carla Rosemberg
Banca: José Carlos de S. Trindade
Banca: Maria Aparecida M. Rodrigues
Resumo: O câncer de próstata (CaP) é a neoplasia mais comumente diagnosticada entre homens no ocidente. Embora tratamentos efetivos para a doença localizada estejam disponíveis atualmente, não há terapia curativa para tumores metastáticos. Além disso, os marcadores diagnósticos utilizados na clínica não conseguem discriminar totalmente a evolução diferencial da doença. Desta forma, o conhecimento das diferenças biológicas entre tumores primários confinados ao órgão e metástases é essencial para o desenvolvimento de novos marcadores e identificação de alvos terapêuticos. Neste estudo a análise baseada na metodologia de HR-CGH cromossômico foi realizada para identificar alterações de ganhos e perdas genômicas em três grupos de amostras: o grupo I, que compreende amostras pareadas de tumor primário e respectivas metástases (11 casos); o grupo II, constituído de pacientes que apresentaram seguimento clínico favorável por mais de 10 anos (5 casos); e o grupo III, constituído por diferentes biópsias do mesmo paciente (5 pacientes com 2 biópsias cada). As amostras foram microdissecadas (amostras a fresco: a partir de lâminas de referência; em blocos de parafina: a laser) e após a obtenção de DNA foram amplificadas (amostras de arquivo: PCR-SCOMP) ou marcadas por nick-translation para a realização de HR-CGH. Os resultados de HR-CGH foram comparados com os dados obtidos da análise de CGH-array num subgrupo de amostras e revelaram concordâncias significativas. Os resultados obtidos na presente investigação revelaram perdas dos cromossomos 1p, 2, 3q, 4p, 5q, 7, 8, 9q, 10q, 11q, 12q, 14q, 15q, 16q, 17q, 18q, 19, 20q e 22q em 80% dos casos avaliados. Além disso, perdas em 17q11.2-25, por exemplo, foram detectadas exclusivamente nos tumores do grupo I e nas suas metástases, e não nos tumores do grupo II, sugerindo que esta alteração deve ser importante... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Prostate cancer (PCa) is the most commonly diagnosed non-cutaneous malignancy and the second leading cause of cancer mortality in men from Occident. Although effective treatments for the localized disease are available, there is no efficient therapy for metastatic tumors. Additionally, clinical diagnostic markers are not able to completely discriminate the differential evolution of the disease. The knowledge of biological differences between localized primary tumors and metastasis can establish new molecular markers and therapeutic targets. In this study, an analysis based on HR-CGH methodology was performed to identify imbalances genomic in three groups of samples: group I, paired samples of primary tumors and its metastasis (11 cases); group II, patients that exhibited favorable follow-up over 10 years (5 cases); and group III, different biopsies from the same patient (5 patients with 2 biopsies each). The tumor samples were submitted to microdissection procedures (fresh samples: from reference slides; paraffin embedded samples: laser), DNA extracted and amplified (archive sample: PCR-SCOMP) or labeled by nick-translation to HR-CGH. The HRCGH results were compared with data obtained from CGH-array analysis of a subgroup of samples and revealed significant concordances. In the present investigation, there were observed losses on chromosomes 1p, 2, 3q, 4p, 5q, 7, 8, 9q, 10q, 11q, 12q, 14q, 15q, 16q, 17q, 18q, 19, 20q and 22q in 80% of the cases. Losses in 17q11.2-25, for instance, were detected exclusively in tumor from group I and its metastasis, but were not found in tumors from group II, suggesting that this alteration must be important in the progression of the disease. Five genes were selected after the comparison between the HR-CGH and CGH-array data. The tumor suppressor genes ARID1A, MTSS1, NME1 and S100A4 and TOP2A (oncogenes) were evaluated by quantitative real time... (Complete abstract click electronic access below)
Doutor
Shah, Sohrab P. "Model based approaches to array CGH data analysis". Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2808.
Texto completoGhaffari, Saeed R. "Development and application of comparative genomic hybridisation (CGH)". Thesis, University of Glasgow, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390763.
Texto completoMohrmann, Inga [Verfasser]. "Array-CGH bei Patienten mit Intelligenzminderung / Inga Mohrmann". Lübeck : Zentrale Hochschulbibliothek Lübeck, 2014. http://d-nb.info/1046429280/34.
Texto completoLee, Sansan. "Genetic counseling perspectives on prenatal array CGH testing". Waltham, Mass. : Brandeis University, 2009. http://dcoll.brandeis.edu/handle/10192/23259.
Texto completoGamero, Angel Mauricio Castro. "Desequilíbrios cromossômicos em nove casos de osteossarcoma detectados através de hibridação genômica comparativa (CGH)". Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-22042013-095920/.
Texto completoOsteosarcoma (OS) is the most frequent aggressive bone malignancy affecting children and young adults with an event-free survival of 50-70% after 3 years. The incidence peak occurs during the second decade of life, suggesting a relationship between rapid bone growth and the development of this tumor. The knowledge of the genetic basis behind tumor progression is still limited. Conventional cytogenetic studies have demonstrated that OS exhibits high cariotipic heterogeneity, with different degrees of aneuploidy and complex structural rearrangements. The CGH is an important tool for studying the genomic profiles of solid tumors, and has confirmed the complexity of cariotipic alterations in OS. However, previous studies have shown divergent results and few have correlated them with tumor progression. The objective of present study was to identify chromosome unbalances in nine samples of OS by CGH. 3 biopsies, 5 resections before quimioterapy and 1 metastasis were analyzed. The experiments were performed accordingly with Kallioniemi et al (1994). CGH detected chromosomal imbalances in all samples. Gains were more frequent than losses. Many chromosomal alterations were observed, especially gains at 1q, xi2, 3p, 4, 5p, 6, 7, 8, 11p, 14q, 16, 21q and X; and losses at 1p, 2q, 3q, 5q, 9q, 11q and 17q. The minimal regions of superposition were gains of 2p13-p14, 2q36-q37, 4q21 and 8p22, and losses of 1p43.2, 3q22-q23 and 3q24. Three patients had consecutive samples, and the chromosomal alterations varied, reflecting the chromosomal heterogeneity for each case. The highest clonal divergence among the consecutive samples was observed between resection and the corresponding metastatic sample, showing the chromosomal complexity acquired during the progression and dissemination in this case. Additional investigations for the characterization of genes at these regions are necessary.
Herr, Alexander [Verfasser]. "Hochauflösende CGH mit Hilfe von DNS-Mikrorastern / Alexander Herr". Berlin : Freie Universität Berlin, 2005. http://d-nb.info/1021667471/34.
Texto completoMarioni, John Carlo. "Statistical methods for array CGH and copy number variation experiments". Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611877.
Texto completoSporns, Peter [Verfasser]. "Korrelation von Array-CGH-Befunden und klinischem Phänotyp / Peter Sporns". Kiel : Universitätsbibliothek Kiel, 2015. http://d-nb.info/1065669992/34.
Texto completoRocha, Ana Laís Bignotto da. "Sequenciamento direto dos genes SIX3, SHH, TGIF1, ZIC2 e array-CGH no estudo de pacientes com holoprosencefalia". Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/61/61132/tde-12112013-150520/.
Texto completoObjective: Analyze through direct sequencing technique the presence of molecular changes on the genes SHH, SIX3, ZIC2 and TGIF1 on individuals with clinical diagnosis of HPE. Analyze through array-CGH technique the presence of molecular changes on individuals with clinical diagnosis of HPE previously submitted to the direct sequencing analyzes. Local: Genetics and Human Cytogenetics Laboratory, HRAC/USP, Bauru-SP. Methods: Were selected 50 individuals from both genders with ages between 03 months and 50 years clinically diagnosed with HPE. Everyone was analyzed through the direct sequencing technique for the genes SHH and TGIF1 completely and for the genes ZIC2 and SIX3 partially. From those individuals which did not have shown changes on the direct sequencing technique, eight individuals with more severe phenotype were selected to the analysis through array-CGH. Results an Discussion: Were analyzed 50 individuals through the technique of direct sequencing of the genes SHH and TGIF1, were found two pathogenic variants in the analysis of SHH gene, in the case 1, the variant p.G24P was identified, and in the case 2 was identified the variant c.1031delC. On the TGIF1 gene were found five polymorphisms already described on the literature. Was identified a new silent variant on the exon 1 of the ZIC2 gene p. Q46Q(c.431G>A) and a polymorphism already described in the literature in two individuals on the gene SIX3. The analysis through array-CGH revealed the presence of one microdeletion in the case 37, of 1,5 Mb on the region 17p12 between the genomic positions 14,052,279-15,102,307. The same deletion was detected in the mother, though this region was never associated to the HPE. Conclusion: The direct sequencing technique is a very important tool for the molecular diagnosis of the HPE, and the direct sequencing standardization for the genes ZIC2 and SIX3 might help in more precise diagnostics on HRAC/USP future studies. The employ of new techniques such as array-CGH may indicate new relations between chromosomal regions and the multiple hit involved in the development of HPE.
Castells, Sarret Neus. "Array CGH com a primera opció per al diagnòstic genètic postnatal". Doctoral thesis, Universitat Autònoma de Barcelona, 2015. http://hdl.handle.net/10803/325159.
Texto completoConventional cytogenetics diagnoses 3-5% of patients with unexplained developmental delay / intellectual disability (DD / ID) and / or multiple congenital Anomalies (MCA). Multiplex ligation probes Amplification (MLPA) increases diagnostic rate between 2.4 to 5.8%. Currently the array comparative genomic Hybridization (CGH) is the highest performing diagnostic tool in patients with DD / ID, MC and autism spectrum disorders. Our aim was to evaluate the efficiency of the use of aCGH as first-line test replacing the karyotype and MLPA in these and other pathological indications (epilepsy, short stature). A total of 1000 patients referred by one or more of the above mentioned disorders were analysed by aCGH using a methodology / strategy hybrid alternative patient versus patients adding support MLPA technique in 50% of patients studied. Following a validation period, an oligoarray platform was chosen. In order to minimize costs and increase efficiency, a patient versus patient hybridization strategy plus MLPA confirmation was used, and analysis criteria were set to optimise detection of pathogenic imbalances. In order to facilitate interpretation of results, a database application named Easy Array was designed. Pathogenic genomic imbalances were detected in 14% of the cases (140/1000), with a variable distribution of diagnosis according to the phenotypes: 18.9% of patients with DD / ID, 13.7% of MCAS, 9.75% of Psychiatric pathologies, 7.01% of patients with Epilepsy and 13.3% of patients with short Stature. Within the MCA, central nervous system abnormalities and congenital heart diseases accounted for 14.9% and 10.6% of diagnosis respectively. Among the Psychiatric disorders, patients with ASD accounted for 8.9% of diagnosis. We can conclude that Array-CGH provides a substantially higher diagnostic yield tan G-banded chromosomes analysis. Its use as first line test and the development of non-standard hybridization strategies reduces consumable costs considerably. Our results demonstrate the effectiveness and efficiency of the use of arrayCGH as the first line test in genetic diagnosis of patients suspected of genomic imbalances, supporting its inclusion within the National Health System.
Kim, Mee Hye. "Optimisation and application of comparative genomic hybridisation (CGH) in cancer cytogenetics". Thesis, University of Glasgow, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272858.
Texto completoZhang, Yunyu. "Hidden Markov Model inference copy number change in array-CGH data". Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33086.
Texto completoIncludes bibliographical references (p. 56-57).
Cancer development and progression typically features genomic instability frequently resulting in genomic changes involving DNA copy number gains or losses. Identifying the genomic location of these regional alterations provides important opportunities for the discovery of potential novel oncogenes and tumor suppressors. Recently, array based competitive genomic hybridization (array-CGH) has become available as a powerful approach for genome-wide detection of DNA copy number changes. Array-CGH assesses DNA copy number in tumor samples through competitive hybridization on microarrays containing probes for thousands of genes. The datasets generated are complex and require statistical methods to accurately define discrete and uniform copy number from the data and to identify transitions between genomic regions with altered copy number. Several approaches based on different statistical frameworks have been developed. However, a fundamental informatic issue in array-CGH analysis remains unsolved by these methods. In particular, sample-specific data compression, a result of tumor cells being commonly admixed with normal cells in many tumor types, must be accounted for in each sample analyzed. Additionally, in order to accurately assess deviations from normal copy number, the copy number readout must be shifted to faithfully represent the baseline copy number in each tumor sample. Failure to appropriately address these issues reduces the accuracy of the data in hard-threshold based high-level analysis.
(cont.) By using the natural framework Hidden Markov Models (HMM) to model the distribution of array-CGH signals, a method infer the absolute copy number and identify change points has been developed to address the above problems. This method has been validated on independent dataset and its utility in inference on array-CGH data is demonstrated here.
by Yunyu Zhang.
S.M.
Jaillard-Herrebrecht, Sylvie. "Place de la CGH-array dans l'étude des anomalies du développement". Rennes 1, 2010. http://www.theses.fr/2010REN1B141.
Texto completoLarré, Stéphane. "Anomalies cytogénétiques impliquées dans la carcinogénèse des tumeurs urothéliales et application clinique". Thesis, Paris Est, 2010. http://www.theses.fr/2010PEST0046.
Texto completoUrothelial carcinomas are the 4th cause of cancer in men, following prostate, colon and lung cancer. An increase of 50% in its incidence was observed on the last 25 years. This cancer presents two types, a superficial type (70% of the cases) of good prognosis and an invasive type (30% of the cases) of bad prognosis. Superficial type require an active monitoring to identify recurrences and evolution to an invasive stage. This follow up is performed using cystoscopy and leads to some level of morbidity and a high cost. An alternative to cystoscopy is possible using urine test to detect cancer cells, but they are lacking of sensitivity to be used instead of cystoscopy in clinical practice. Our goal was to develop a urine detection tool of urothélial carcinomas.Material and MethodsUrothelial carcinoma usually present with a high level of genetic instability. We first analyse literature so to identify most relevant cytogenetic abnormalities that occur in urothélial carcinomas. A CGH array chip was designed using 341 clones (BAC) that were selected according to initial analysis. This chip called BCA-1 covers the whole genome and was developed in collaboration with ArrayGenomics (Voisins Le Bretonneux, France).ResultsThis test has shown a good efficacy on a preliminary study of cytogenetic analysis on 10 cancerous and benign bladder cell lines. The Chip was then assessed in clinical practice on a series of 163 patients diagnosed with or without urothelial cancer. Urines were collected and analysed using the BCA-1 chip. A software was designed to favour homogeneous and detailed clinical data collection and take into consideration the complex management of the tumours.The test using the CGH chip as shown an excellent diagnosis performance with a sensitivity of 96% and a specificity of 98% for bladder cancer detection, and a sensitivity of 100% on upper urinary tract detection.Finaly, the test was able to define the grade of the tumour according to cytogenetic loci affected. This grade was strongly correlated with the pathology score and could be used to predict outcomes in upper urinary tract carcinomas. Our work lead to the developpement and the analysis of a new urothélial carcinoma urinary detection test, to the identification of the agressivity of the tumour, and to the development of an analysis and data entry software for clinical details
Grzesiuk, Juliana Dourado. "Caracterização Citogenética Molecular de Rearranjos Cromossômicos Aparentemente Equilibrados Associados ao Fenótipo de Infertilidade". Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-22042013-151132/.
Texto completoReciprocal translocations are the most common balanced rearrangement in humans. Often individuals with balanced rearrangements show no clinical findings. However, in meiosis, the pairing between translocated chromosomes forms a quadrivalent cross-shaped figure which has the effect of making chromosome disjunction uncertain and, depending on the rearrangement, and on the segregation of the unbalanced chromosomes, the individual can be infertile, can present with an increased risk of spontaneous abortions or can have an offspring with abnormal phenotype. We have studied two families of infertile patients, who were carriers of chromosomal translocations. The objective was to characterize the cytogenetic and cytogenomic alterations related to male infertility in patients with apparently balanced rearrangements using classical cytogenetic techniques (GTG banding), molecular cytogenetics (FISH) and cytogenomics (array-CGH). Seven subjects of the family 1 were studied, including three carriers of translocation (X;22), one azoospermic. Two cases of mosaicism for Turner syndrome were detected in this family. The second family consisted of two oligozoospermic brothers with translocation (8;13). FISH was used to characterize the karyotypes as 46, XX or 46,XY, t(X;22)(p22.3;q11.2) for the members of the family 1 and 46,XY,t(8;13)(q13;q14) for family 2. Array-CGH was also performed using the Agilent platform 2x400K, to detect associated copy number variations of some of the candidate genes that could be related to infertility. In the family 1 the candidate genes were 132 piRNAs sequences and DDX11,Jagged 2 and ADAM18 genes. The candidate genes for the family 2 were ADAM18 and POT.
Picard, Franck. "Segmentation/classification de processus. Application a l'analyse de donnees de microarrays CGH". Phd thesis, Université Paris Sud - Paris XI, 2005. http://tel.archives-ouvertes.fr/tel-00116025.
Texto completoest de partitionner des données en zones homogènes, et de regrouper ces zones en un nombre fini de classes. Les problèmes de segmentation/classification sont traditionnellement étudiés à l'aide
des modèles de chaînes de Markov cachées. Nous proposons un modèle alternatif qui combine un modèle de segmentation et un modèle de mélange.
Nous construisons notre modèle dans le cas gaussien et nous proposons une généralisation à des variables discrètes dépendantes. Les paramètres de ce modèle sont estimés par maximum de vraisemblance à l'aide d'un algorithme hybride fondé sur la programmation dynamique et sur l'algorithme EM. Nous abordons un nouveau problème de sélection de modèle qui est la sélection simultanée du nombre de groupes et du nombre de segments et proposons une heuristique pour ce choix.
Notre modèle est appliqué à l'analyse de données issues d'une nouvelle technologie, les microarrays CGH (Comparative Genomic Hybridization). Cette technique permet de compter le nombre de milliers de gènes le long du génome en une seule expérience. L'application de notre méthode à ces données permet de localiser des zones délétées ou amplifiées le long des chromosomes. Nous proposons également une application à l'analyse des séquences d'ADN pour l'identification de régions homogènes en terme de composition en nucléotides.
Glentis, S. "Whole genome amplification for PGD and PND : molecular and a-CGH diagnosis". Thesis, University College London (University of London), 2009. http://discovery.ucl.ac.uk/18554/.
Texto completoPicard, Franck. "Segmentation-classification de processus : application à l'analyse des données de microarrays CGH". Paris 11, 2005. http://www.theses.fr/2005PA112186.
Texto completoThis thesis is devoted to the development of a new statistical model for segmentation/clustering problems. The objective is to partition the data into homogeneous regions and to cluster these regions into a finite number of groups. Segmentation/clustering problems are traditionally studied with hidden Markov models. We propose an alternative model which combines segmentation models and mixture models. We construct our model in the Gaussian case and we propose a generalization to discrete dependent variables. The parameters of the model are estimated by maximum likelihood with a hybrid algorithm based on dynamic programming and on the EM algorithm. We study a new model selection problem which is the simultaneous selection of the number of clusters and of the number of segments. We propose a heuristic for this choice. Our model is applied to the analysis of CGH microarray data (Comparative Genomic Hybridization). This technique is used to measure the number of thousands of genes on the genome in one experiment. Our method allows us to localize deleted or amplified regions along chromosomes. We also propose an application to the analysis of DNA sequences for the identification of homogeneous regions in terms of nucleotide composition
Fuhrmann, Christine. "Entwicklung der Array-CGH zur hochauflösenden, genomweiten Untersuchung von DNA-Veränderungen einzelner Tumorzellen". Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-89535.
Texto completoDavey, Robert Paul. "Refinement and validation of algorithms for deduction of gene content from CGH microarrays". Thesis, University of East Anglia, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.429607.
Texto completoMorris, J. A. "A bioinformatics framework for management and analysis of high throughput CGH microarray projects". Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1364856/.
Texto completoFuhrmann, Christine. "Entwicklung der Array-CGH zur hochauflösenden, genomweiten Untersuchung von DNA-Veränderungen einzelner Tumorzellen". kostenfrei, 2008. http://edoc.ub.uni-muenchen.de/8953/.
Texto completoRichard, Frank. "Chromosomale Imbalancen invasiv duktaler und invasiv lobulärer Mammakarzinome detektiert mittels komparativer genomischer Hybridisierung (CGH)". [S.l.] : [s.n.], 1999. http://deposit.ddb.de/cgi-bin/dokserv?idn=96200166X.
Texto completoRichard, Frank. "Chromosomale Imbalancen invasiv duktaler und invasiv lobulärer Mammakarzinome detektiert mittels komparativer genomischer Hybridisierung (CGH)". Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 1999. http://dx.doi.org/10.18452/14599.
Texto completoThe aim of the study was to analyze invasive ductal and invasive lobular breast carcinomas regarding to molecular DNA imbalances as well as different DNA imbalances in tumor subgroups of the invasive ductal carcinomas. Comparative genomic hybridization (CGH) was applied to analyze 30 invasive ductal and 20 invasive lobular breast carcinomas to carry out genetic alterations. In both tumor subgroups, DNA losses showed a higher incidence compared to DNA gains, suggesting a higher influence of inactivation of tumor suppressor genes in tumor progression. Invasive ductal carcinomas showed a higher incidence of alterations per case compared to invasive lobular carcinomas (14,9 vs. 8,9). Besides a higher incidence of DNA losses, particularly DNA gains were statistically significant in invasive ductal carcinomas (6,2 per tumorcase vs. 2,7 per tumorcase). DNA gains on chromosome 1q and DNA losses on chromosomes 6q, 11q22-qter and 13q were investigated in >=40% of all tumor cases. DNA gains were observed with a higher frequency in invasive ductal carcinomas on 6p, 8q, 11q13, 16p, 17q, 19p/q and 20q. Additionally, DNA losses showed a higher incidence on 2q, 3p, 4p/q, 5q, 7p, 8p, 9q, 10q and 15q compared to invasive lobular carcinomas. In contrast, DNA losses on 16q, 17p, 18q and 22q reached statistical significance in invasive lubular carcinomas. Well-differentiated (G1) and poorly differentiated (G3) invasive ductal carcinomas reflected different genetic imbalances. Well-differentiated carcinomas are associated with DNA gains on 1q, 11q11-13, 16p and 20q, whereas poorly differentiated tumors showed additional DNA losses on 5q, 18q and 21q21. Furthermore, the investigation indicated that the average number of alterations is correlated also to the estrogen receptor content of the invasive ductal carcinomas. Tumors with estrogen receptor negative content showed a higher incidence of alterations on the following regions, i.e., DNA gains on 1p, 6p and 22q and DNA losses on 5q, 7p, 8p and 12q. Consequently, invasive ductal and invasive lobular carcinomas are characterized by distinct patterns of chromosomal alterations.
Goeze, Almut. "Charakterisierung chromosomaler Imbalancen in Adenokarzinomen der Lunge mit Hilfe der Comparativen genomischen Hybridisierung (CGH)". Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2000. http://dx.doi.org/10.18452/14568.
Texto completoAdenocarcinomas are the most common non small cell lung carcinomas worldwide with increasing incidence especially in women. For the genetic analysis of this tumor type we screened 60 primary tumors and additionally 23 metastases from 10 cases (4 corresponding metastases per primary tumor as maximum) by Comparative Genomic Hybridization (CGH). The following alterations were found in over 50% of the 60 primary tumors: Deletions on chromosomes 3p, 4p, 4q, 5q, 6q, 8p, 9p, 9q, 13q, 15q, and 18q as well as overrepresentations on chromosomes 1q, 5p, 8q, 11q. 17q. 19q und 20q. The most frequent alteration was the overrepresentation on chromosome 1q22-q23 (73,3%), followed by overrepresentations on chromosomes 20q11.2-q13.2 (66,7%), and 8q23-q24.1 (61,7%), and deletions on 3p22-p21 (61,7% ), 4q26-q28 (63,3%), 6q16 (60,0%), 6q22 (60,0%), 9p13-p21 (63,3%), 13q21 (68,3%), and 13q31 (68,3%). At the comparison between 24 non metastasizing primary tumors versus 23 metastasizing tumors and 10 metastases the following changes were statistically significant (c2 test) associated with the metastasizing phenotype: deletions on chromosomes 3p22-p25, 4p13-p15.1, and 17p12-p13, as well as overrepresentations on 1q21, 11q12-13, 14q11.1-q13, 15q24, and 20q12-13.1 whereas the deletion on chromosome 19p13.1-p13.3 and overrepresentations on chromosomes 3p12-p14 , 4q26-q28, and 5p14 were associated with the non metastasizing phenotype. A clonal relationship could be shown in every case with primary tumor and corresponding metastases. In summary, adenocarcinomas of the lung are characterized by recurrent patterns of chromosomal imbalances allowing a correlation between tumor genotype and tumor phenotype.
Rooney, Patrick Hugh. "A genomic approach to the study of chemoresistance". Thesis, University of Aberdeen, 2000. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602009.
Texto completoPiard, Juliette. "Déficience intellectuelle : identification de nouveaux gènes par une approche multicentrique". Thesis, Bourgogne Franche-Comté, 2018. http://www.theses.fr/2018UBFCE005.
Texto completoIntellectual disability (ID) impacts 1 to 3% of the general population with an excess of affected males. This condition is characterized by an extreme clinical and genetic heterogeneity making the deciphering of its causes more complex. The technological revolution that took place in the study of the genome over the last two decades has provided a useful tool for identification of new genetic entities. This is particularly true for chromosomal micro-array analysis since early 2000s and for next generation sequencing since 2011. We took advantage of this by identifying the molecular basis of three singular conditions. We applied a structured methodology and created a network of collaborations to define or confirm these new ID syndromes. 1. Whole exome sequencing alongside with array-CGH 2.Identification of a candidate gene sequence alteration in the index case and other affected patients of the family 3.Constitution and study of a replication cohort 4.Biochemical studies and/or animal models in order to support the assumption of causalityBased on this research strategy, we were able to complete the following projects : Discovery of a syndromic form of autosomal recessive ID associated with cervical spine defects due to bi-allelic CDK10 mutations. Identification of an ATAD1-related profound and lethal autosomal recessive encephalopathy with stiffness and distal arthrogryposis. Characterization of a FRMPD4-related X-linked non-syndromic ID
Delahaye-Duriez, Andrée. "Identification de nouveaux gènes impliqués dans des maladies ophtalmologiques rares en utilisant la CGH-array". Paris 7, 2011. http://www.theses.fr/2011PA077066.
Texto completoThe karyotype detects a chromosomal anomaly in 7. 7% to 10% of neonates with ocular birth defect. The introduction of microarray technology showed a very high rate of rearrangements below the resolution of karyotyping. My objectives in this work were to characterize using comparative genome hybridisation-based microarray analysis (array-CGH) chromosomal regions involved in rare ophthalmologic disorders, and then to identify new genes. In the first part of my work, we performed array-CGH in 65 patients presenting syndromal ocular developmental anomalies. A causal or potentially causal anomaly was found for 15% of them. Four had a pathogenic deletion involving a gene known to be involved in ocular anomalies (FOXC1 or OTX2}, while 4 others had a pathogenic deletion not classically associated with ocular malformations: del(17)(pl3. 3p!3. 3), del(10)(pl4p!5. 3) and del(16)(pl 1. 2pl 1. 2). In collaboration with other teams, we gathered patients to study genotype-phenotype correlations for 6p25 and 17pl3. 3 deletions. The second part of my work focused on a candidate gene study: ARHGEF26. Sequencing this gene in other patients with similar phenotype and studying the index patient family segregation, we could not demonstrate the ARHGEF26 involvement in this phenotype. This second part highlights the limits and difficulties of gene identification using array-CGH. These results demonstrate that array-CGH-based chromosomal analysis, beyond its importance for diagnosis and genetic counselling, can help to establish new genotype-phenotype correlations for chromosomal anomalies as well as identify potential new regions involved in rare ophthalmologic disorders
RASSU, STEFANIA. "Utilità clinica dell’array-CGH nello studio di pazienti in età pediatrica con Leucemia Linfatica Acuta". Doctoral thesis, Università degli Studi di Cagliari, 2016. http://hdl.handle.net/11584/266634.
Texto completoKreuz, Markus. "Entwicklung und Implementierung von Auswertungswerkzeugen für Hochdurchsatz-DNA-Kopienzahl-Analysen und deren Anwendung auf Lymphomdaten". Doctoral thesis, Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-161664.
Texto completoArmengol, Rosell Gemma. "Detecció de guanys i pèrdues de material genètic en tumors sòlids". Doctoral thesis, Universitat Autònoma de Barcelona, 2000. http://hdl.handle.net/10803/3685.
Texto completoCoe, Bradley P. "The role of specific genomic alterations in small cell lung cancer aggressiveness". Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2283.
Texto completoMóz, Luis Eduardo Silva. "Caracterização genômica do Edema de Reinke". Botucatu, 2017. http://hdl.handle.net/11449/149913.
Texto completoResumo: Introdução: o Edema de Reinke (ER) é uma lesão laríngea considerada benigna relacionada ao tabagismo. Dados em literatura relatam associações entre o ER e a detecção de diferentes graus de displasia e carcinoma in situ, bem como alterações na imunoexpressão de proteínas tumorais como a p53. Alguns autores classificam o ER entre as lesões pré-malignas, com risco de transformação e progressão para carcinoma de laringe. Não havendo consenso na literatura, torna-se necessária a realização de estudos moleculares. Objetivos: caracterizar o perfil genômico global de alterações no número de cópias do DNA em amostras de pacientes com ER. Métodos: oito amostras removidas por microcirurgia foram submetidas à extração do DNA. Os perfis de alteração no número de cópias genômicas e os genes candidatos associados foram analisados pela metodologia da hibridação genômica comparativa (CGH array), utilizando-se a plataforma de 4x180K (Agilent Technologies). Os dados de microarranjos foram analisados utilizando o programa CytoGenomics v4.0.2.21 (Agilent Technologies). As alterações no número de cópias (CNAs) obtidas foram comparadas com o banco de dados Database of Genomic Variants (DGV). A classificação dos genes selecionados para análise foi realizada baseada em dados descritos no National Center for Biotechnology Information (NCBI). Resultados: Foram encontrados perdas, ganhos ou deleções em 54 genes, um RNA não codificador longo intergênico (lincRNA), seis sequências hipotéticas e 10 microRN... (Resumo completo, clicar acesso eletrônico abaixo)
Doutor
Lohan, Silke [Verfasser]. "Analyse von genomischen Aberrationen mit hochauflösender Array-CGH bei Patienten mit Fehlbildungen der Extremitäten / Silke Lohan". Berlin : Freie Universität Berlin, 2013. http://d-nb.info/1031190546/34.
Texto completoMachado, Isabela Nelly. "Detecção de instabilidade genômica por hibridização genômica comparativa baseada em microarranjos (array CGH) em fetos dismórficos". [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/311739.
Texto completoTese (doutorado) - Universidade Estadual de Campinas. Faculdade de Ciências Médicas
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Resumo: Introdução: Para uma parcela significativa de fetos com defeitos congênitos o diagnóstico sindrômico permanece indefinido, dificultando a abordagem perinatal, o estabelecimento de prognóstico e o aconselhamento genético. A incapacidade de detecção de pequenas instabilidades genômicas, atualmente apontadas como provável fator causal nestas condições dismórficas, é a principal limitação do estudo cromossômico microscópico pelo bandamento G (cariótipo convencional). A hibridização genômica comparativa (comparative genomic hybridization-CGH) é capaz de identificar perdas e ganhos de material genômico com alta resolução, sem envolver o cultivo celular e o conhecimento prévio da região genômica envolvida. Objetivo: Avaliar a aplicabilidade da técnica de array CGH em sangue fetal para o diagnóstico de perdas e ganhos genômicos em um grupo de fetos dismórficos. Sujeitos/Método: Foi realizado um estudo prospectivo descritivo a partir de amostras sanguíneas de fetos dismórficos e com cromossomos numericamente normais ao bandamento G, admitidos no Setor de Medicina Fetal do Centro de Atenção Integral à Saúde da Mulher (CAISM) da Universidade Estadual de Campinas (Unicamp). Foi realizada a caracterização da amostra estudada e uma análise descritiva dos achados moleculares através da técnica de array CGH. Resultados: Foram incluídos no estudo 50 fetos, dos quais 49 preencheram os critérios de qualidade da técnica. A taxa de detecção de alterações cromossômicas pela técnica de array CGH não detectadas pelo cariótipo convencional foi de 93,7% (45 fetos), e 27% foram consideradas significativas dos pontos de vista citogenético e clínico. Entre os fetos com alterações do número de cópias, 87% apresentaram pelo menos um clone para o qual já estão descritas variações do número de cópias (CNV) em indivíduos fenotipicamente normais. Adicionalmente, a técnica mostrou-se eficaz para o esclarecimento diagnóstico da origem, exata localização e dimensionamento do material adicional encontrado em um feto com anomalia cromossômica estrutural. Conclusões: A caracterização do perfil genômico por array CGH de fetos com defeitos congênitos permitiu complementar o diagnóstico citogenético convencional, aumentando a definição diagnóstica e a identificação de regiões cromossômicas associadas a algumas anomalias congênitas
Abstract: Introduction: A great number of fetuses with congenital defects remain without definitive diagnosis, making difficult the perinatal management, the prognosis establishment and the genetic counseling. The incapacity of detection of short sequence copy number changes, pointed as a probable etiology factor for some congenital defects, is the main limitation of routine G-banding. The Comparative Genomic Hybridization (CGH) overcome this limitation, and also does not require cellular culture or prior knowledge of the involved genomic region. Objective: To evaluate the applicability of the CGH method on fetal material for genomic gains and losses in a group of malformed fetuses. Methods: On a prospective descriptive study, fetal blood samples were collected from malformed fetuses with numerically normal chromosomes at G-banded karyotype, at the Fetal Medicine Unit of the Centro de Atenção Integral à Saúde da Mulher (CAISM) of the Universidade Estadual de Campinas (UNICAMP). Sample characterization and a descriptive analysis of the CGH-based technique results were accomplished. Results: Fifty fetuses were included in this study and 49 were considered optimal according to adopted quality control criteria. The detection rate of fetuses with copy number imbalances not detected by the G-banded karyotype was 93.7% (45 fetuses), with 27% of cytogenetic and clinical significance. Among fetuses with copy number imbalances, 87% presented at least one abnormal clone encompassing CNVs described for phenotipically normal individuals. Additionally, the array CGH showed to be effective for the identification of the additional genetic material origin, with its precise location and size, presented in one fetus with structural chromosomal anomaly. Conclusions: The genomic profile characterization of malformed fetuses through array CGH allowed complementing the conventional cytogenetic diagnosis, obtaining a higher precise diagnosis and the identification of chromosomal regions associated with some congenital anomalies
Doutorado
Tocoginecologia
Doutor em Tocoginecologia
Pinato, Claudia. "ARRAY-CGH COME ESAME DI PRIMO LIVELLO NELLA DIAGNOSI MOLECOLARE DI RITARDO MENTALE E ANOMALIE CONGENITE". Doctoral thesis, Università degli studi di Padova, 2015. http://hdl.handle.net/11577/3424644.
Texto completoLa tecnica di array-CGH si è affermata negli ultimi anni come un potente strumento per l’identificazione delle cause molecolari alla base di fenotipi complessi caratterizzati da disabilità intellettive, autismo, epilessia, disordini psichiatrici e anomalie congenite multiple. Negli ultimi 10 anni, infatti, è emerso sempre più chiaramente che l’analisi citogenetica convenzionale non è in grado di rilevare riarrangiamenti inferiori alle 5-10 Mb che possono essere responsabili di tali fenotipi clinici. Questo limite è stato superato dall’array-CGH che ha aumentato del 15-20% la detection rate di sbilanciamenti cromosomici criptici (delezioni o duplicazioni). La possibilità di avere una tecnica di tipo genome wide ad elevata risoluzione ha portato alla proposta, nel 2010, da parte dell’International Standard Cytogenomic Array (ISCA) Consortium, dell’utilizzo di tale tecnica come esame di primo livello in individui con disabilità intellettive e anomalie congenite. Dagli studi effettuati con tecnologia microarray è risultato evidente che esistono regioni cromosomiche in cui sono particolarmente frequenti ricombinazioni aberranti, dovute alla presenza di segmenti con un’elevata omologia di sequenza che causano un alto grado di instabilità genomica. L’utilizzo dell’array-CGH ha inoltre rivelato la presenza nel genoma di un elevato numero di variazioni strutturali, di dimensioni maggiori di 1Kb, chiamate copy number variations (CNVs), le quali, essendo state identificate anche in individui sani, non sempre rappresentano una causa diretta di malattia. Questa difficoltà nell’interpretazione della patogenicità delle CNVs è ancora più rilevante in diagnosi prenatale poiché si traduce in una incertezza in termini prognostici sulla salute del feto. Per questo motivo, nonostante i vantaggi dati dalla tecnica, l’array-CGH in diagnosi prenatale viene, al momento, considerato un test di secondo livello da utilizzare in associazione all’analisi citogenetica convenzionale. In questo studio sono stati valutati, mediante array-CGH, 1051 pazienti che presentano ritardo mentale e/o dello sviluppo, autismo, anomalie congenite multiple e dimorfismi. L’obiettivo principale è stato quello di verificare la presenza di riarrangiamenti cromosomici criptici in modo da dimostrare l’utilità dell’impiego di microarray genomici come esame di primo livello per la caratterizzazione delle cause molecolari alla base del fenotipo patologico degli individui. Sono stati poi ipotizzati i meccanismi di formazione delle anomalie verificando, mediante l’analisi dei breakpoints, la presenza di regioni di omologia che possano aver predisposto al riarrangiamento. Quindi è stato valutato se il meccanismo di formazione e il significato clinico delle CNVs identificate possano essere correlati al pattern di ereditarietà, al tipo o alle dimensioni dello sbilanciamento. I risultati ottenuti mostrano che il 15.8% dei casi analizzati è portatore di una anomalia patologica o VOUS (variant of uncertain significance) verosimilmente patologica, e che queste sono più frequentemente delezioni e CNVs insorte de novo. È stato inoltre evidenziato che sia il significato clinico delle CNVs sia il loro meccanismo di formazione possano essere correlati alle dimensioni degli sbilanciamenti. È stata successivamente analizzata la distribuzione delle CNVs nei diversi cromosomi ed è emerso che in alcuni di essi la densità di anomalie riscontrate è maggiore rispetto agli altri. L’applicazione dell’array-CGH in un elevato numero di pazienti ha permesso, inoltre, di stimarne la sensibilità nell’identificazione di mosaicismi, sebbene abbiano una frequenza inferiore all’1% in individui con disabilità intellettive. È stato osservato che la tecnica è in grado di rilevare anomalie che coinvolgono anche un numero limitato di cellule, fino al 10%. Infine sono stati analizzati alcuni campioni fetali di villi coriali e liquido amniotico per valutare il possibile utilizzo dei microarray genomici in diagnosi prenatale. Il numero esiguo di campioni analizzati non ci ha permesso di trarre delle conclusioni, tuttavia, per le difficoltà che si riscontrano nell’interpretazione del significato clinico delle CNVs, è da ritenere al momento un test di secondo livello da utilizzare in associazione al cariotipo standard.
Ribeiro, Cintia Marques. "Estudo de genes candidatos aos Transtornos do Espectro Autista". Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-06092013-153442/.
Texto completoThe 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
Dimassi, Sarra. "Identification de gènes responsables d'épilepsies de l'enfant". Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1114.
Texto completoEpilepsy is a chronic neurological disorder characterized by repeated epileptic seizures, a sign of cortical neurons paroxysmal hyperactivity. In recent years, several monogenic genes involved in epilepsy have been identified. The aim of our work is to identify new genetic abnormalities responsible for childhood epilepsies. This work is divided into four complementary studies. First, we searched copy number variation (CNV) by pangenomic exploration of a cohort of 47 patients with Rolandic epilepsy (RE) using CGH array. We identified several CNVs carrying genes involved in epilepsy, including PRRT2 and GRIN2A (genes). Secondly, the same approach was applied to a cohort of 8 Tunisian patients with infantile spasms. It allowed the identification of a 9q34.3 deletion includingEHMT1, implicated in Kleefstra syndrome and a 15q13.1 duplication, known to be involved in neurodevelopment disorders. For the third study, we compared two library-building methods for a gene-targeted panel for the diagnosis of Monogenic childhood epilepsies, in a cohort of 24 epileptic patients. This approach allowed us to develop a coverage analysis software, which we named DeCovA. In the last study, we used a trio-based exome-sequencing approach to look for de novo mutations in 10 patients with infantile spasms. We found de novo pathogenic variants in four patients, involving KCNQ2, SCN1A, NR2F1, and ALG13. Our results confirm the increasing role of genetics and the major interest of new technologies in the etiological exploration of childhood epilepsy
Vogazianou, Artemis P. "Analysis of chromosome 1 status in human oligodendrocytic, oligoastrocytic and astrocytic gliomas, using tiling-path CGH-microarray". Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614682.
Texto completoBaker, Serena F. "Assessment of aCGH Clustering Methodologies". BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2644.
Texto completoOliveira, Jakeline Santos. "Determinação das alterações genômicas em pacientes com malformações congênitas". Botucatu, 2018. http://hdl.handle.net/11449/180587.
Texto completoResumo: As ACs são alterações visíveis nos cromossomos, classificadas como numéricas e estruturais. Atualmente o grande desafio da genética clínica é classificar e associar a relevância clínica dos desequilíbrios genéticos ao fenótipo dos portadores. O trabalho tem como objetivo principal caracterizar desequilíbrio genômico sem diagnóstico sindrômico previamente descritos pelas técnicas de citogenética clássica, molecular visando apurar os pontos de quebras e genes inseridos na região cromossômica alterada por meio da citogenômica em estudos de casos. Foram feitas análises por citogenética (bandamento GTG), citogenética molecular (FISH) e citogenômica (array-CGH) em três pacientes com malformações congênitas não-sindrômicas para definição diagnóstica e maior conhecimento sobre a correlação genótipo-fenótipo. Foram redigidos estudos de casos de três pacientes portadores de MCs, atraso do desenvolvimento e deficiência intelectual. O primeiro copilado de caso trata-se de paciente do sexo feminino com anomalias esqueléticas, deficiência intelectual e atraso do desenvolvimento. O cariótipo da paciente é 46,XX[11]/47,XX,+mar[9]. A análise de array-CGH revelou dois ganhos/duplicações nas bandas cromossômicas 6p11.2q12 (10.335 Mb de tamanho) e 6q14.1q14.3 (10.765 Mb de tamanho). Por meio da técnica da FISH e os resultados do array-CGH a região duplicada 6q14.1q14.3 encontra-se inserida em um cromossomo marcador, oriundo do cromossomo 6. Os sinais clínicos descritos na paciente foram semelhan... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The ACs are visible changes in the chromosomes, classified as numerical and structural. Currently the great challenge of clinical genetics is to classify and associate the clinical relevance of genetic imbalances with the phenotype of the carriers. The main objective of this work is to characterize genomic imbalance without syndromic diagnosis previously described by the classical and molecular cytogenetic techniques, in order to determine the breakpoints and genes inserted in the chromosomal region altered by cytogenetics in case studies. Cytogenetics (GTG banding), molecular cytogenetics (FISH) and cytogenetics (array-CGH) were performed in three patients with non-syndromic congenital malformations for diagnostic definition and greater knowledge on genotype-phenotype correlation. Case studies of three patients with MCs, developmental delay and intellectual disability were written. The first case file is a female patient with skeletal anomalies, intellectual disability and developmental delay. The patient's karyotype is 46, XX [11] / 47, XX, + sea [9]. The array-CGH analysis revealed two gains / doublings in the chromosomal bands 6p11.2q12 (10,335 Mb in size) and 6q14.1q14.3 (10,765 Mb in size). Through the FISH technique and the results of the array-CGH the duplicate region 6q14.1q14.3 is inserted in a chromosome marker, coming from chromosome 6. The clinical signs described in the patient were similar to other patients with duplication of the region 6q14. The genes PGM3, M... (Complete abstract click electronic access below)
Mestre
Morice-Picard, Fanny. "Etude clinique et génétique de l’albinisme oculocutané : développement d’outils de diagnostic moléculaire et recherche de nouveaux gènes". Thesis, Bordeaux 2, 2013. http://www.theses.fr/2013BOR22101/document.
Texto completoOur work focused on oculocutaneous albinism (OCA) by studying its clinical and molecular aspects. Despite a thorough analysis of the known genes involved in oculocutaneous albinism, 15% of patients remain without diagnostic at the molecular level indicating that mutations are located in unexplored regions and are undetected by standard techniques or that other genes are involved in albinism. We established a clinicomolecular database describing more than 400 patients and developped molecular tools in order to improve molecular diagnostic including a custom high resolution array-CGH dedicated to the four OCA genes (TYR, OCA2, TYRP1 and SLC45A2). We also used different strategies to identify new genes. Array-CGH allows us to detect large deletion in TYR, OCA2 and SLC45A2 and a complexe rearrangement in OCA2 in 2 unrelated patients. We identified, in 5 patients presenting with a non syndromic OCA, mutations in SLC24A5, recently associated with OCA6. Exome sequencing of 6 different patients allows us to identify candidate genes, for which further studies are required to confirm their involvement in OCA pathogenesis. The results of this work allowed us to delineate clinical and genetics aspects of more than 400 OCA patients and to identify new molecular mechanisms leading to OCA and candidates genes for which exact nature of their functions has to be understood. Giving the complexity of pigmentary system development and its regulation, identification of new genes leading to OCA could help to better understand OCA and take care of patients
Birnbaum, David. "Altérations moléculaires dans l'adénocarcinome du pancréas". Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM5088.
Texto completoPancreatic adenocarcinoma (PDCA) is a major public health problem in France and worldwide. The inoperability and the poor prognosis of the PDCA are due to late diagnosis, rapid tumor progression (>80% of patients displayed metastases at diagnosis), early recurrences after resection, and poor response to available therapies. Innovative approaches and a comprehensive characterization of molecular genetic alterations are dearly needed to help develop techniques of early detection, identify new molecular targets and devise novel targeted-therapies (Hidalgo, 2010). Using high-resolution array-comparative genomic hybridization (aCGH), we studied the genome alterations of 39 fine-needle aspirations from PDCA. Recurrent losses were observed and comprised several known tumor suppressor genes. We identified frequent genetic gains. With this study, we decided to go one step further by identifying genes that might also be deregulated at the transcriptomic level. We started our analysis with a population of PDCA (n=419) versus normal pancreas (n = 105). Among the 352 genes found amplified and/or gained by aCGH, 170 (48%) were up regulated at the transcriptional level in PDCA compared to normal pancreatic tissues. Major pathways involved were cell cycle, TP53 and TGFß. Among the genes located in regions of losses, 141 (41%) were down regulated in PDCA compared to normal tissues. Furthermore, some genes were found related to a patients' survival With this study, we highlighted novels genes associated to PDCA oncogenesis. Some of those candidates should be further investigated as prognosis markers or as potential targets for new therapeutic approaches
Joaquim, Tatiana Mozer. "Correlação cariótipo-genótipo-fenótipo de rearranjo cromossômico estrutural familiar envolvendo as regiões 4p e 12q". Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-04012017-114707/.
Texto completoStructural chromosomal rearrangements are potentially associated with the development of genetic disorders due to disruption, inactivation or gene dosage alterations. The objective of this project was to perform the genomic characterization of a familial structural chromosomal rearrangement involving the short arm of chromosome 4 and the long arm of chromosome 12 in two patients and carriers. The experimental approach involved using a combination of classical cytogenetic techniques (GTG banding), molecular cytogenetics (FISH) and cytogenomics (array-CGH), to provide a diagnostic definition and a better understanding of how changes in the karyotype and genotype may be associated with the phenotype. Six individuals were evaluated, two patients with phenotypic abnormalities, as well as the carriers of an apparently balanced 4p;12q translocation with normal phenotypes. Although the two patients showed a common chromosomal abnormality, the derivative chromosome 4 [der (4)], they presented distinct phenotypic findings. The investigation provided a definition of the diagnosis of 4p16 deletion and trisomy 12qter for the two patients with abnormal phenotypes and a karyotype 46,XX,der(4)t(4;12)(p16;q24.3). In addition a precise definition of the breakpoints at 4p16.3 and 12q24.31->q24.33, and the parental origin of the rearrangement was determined. A precise definition of the cytogenetic diagnosis of four carriers with an apparently balanced translocation and karyotype t(4;12)(4pter->4p16.3::2q24.31->12qter; 12qter 12q24.31->4pter::4p16.3), facilitated the genetic counseling for the family. In both patients, the array-CGH technique (2x400K Platform, Agilent®) detected a subtle difference in size between losses and gains in the chromosomal regions involved in the rearrangement. Patient 1 presented a loss of 2,707,221 bp in the cytoband 4p16.3, and a gain of 12,405,205 bp in 12q24.31->q24.33. Patient 2 had a loss of 2,710,969 bp in 4p16.3 and a gain of 12,393,885 bp in 12q24.31 -> q24.33. Both regions of genomic imbalance included genes that may be relevant to phenotypic findings observed in our patients, including: WHSC1, NELFA, LETM1, FGFRL1 and SPON2. Genomic findings also confirmed the presence of a balanced translocation in four carriers, with no genomic losses and/or gains in the regions of chromosome breakpoints. The results of the investigation of the methylation pattern of FGFRL1 and SPON2 genes could not demonstrate that repression of gene expression due to maternal and paternal imprinting was associated with the distinct phenotypes observed in the two patients. Although it has been possible to indicate genes related to the phenotype of the patients, the correlation between the genetic alteration and phenotype may depend on the synergistic action of multiple genes from more than the 190 involved in this familial chromosomal rearrangement.
Grzesiuk, Juliana Dourado. "Investigação genômica de pacientes inférteis com oligozoospermia". Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-30032017-162247/.
Texto completoInfertility affects about 15% of the couples, and it is currently recognized, that male factors are involved in about 50% of cases. Changes in seminal parameters are detected in most infertile men and the most common alteration, known as oligozoospermia, is a low concentration of sperm in the ejaculate. Several studies show a strong relationship between genetic factors and infertility, including chromosomal abnormalities and microdeletions of Y chromosome, however, the causes of oligozoospermia remain unclear. The development of new research technologies has allowed the detection of changes at genomic levels, such as mutations and copy number variations (CNVs). This study aimed to perform a genomic characterization of patients with idiopathic oligozoospermia to determine whether there is a correlation between changes of copy number and losses of heterozygosity (LOHs) in relation to the phenotype of infertility. Eighteen patients were selected for the cases after rigorous clinical examination and investigation of their reproductive history. Patients with chromosomal abnormalities or microdeletions of the Y chromosome were excluded. Six proven fertile men comprised the control group. Genomic investigation of both groups was performed by microarray comparative genomic hybridization (aCGH) using 4X180K platform (Agilent, US) analysed by Nexus 8.0 software. Potential pathogenic changes were detected on Y chromosome, as well as on the X and autosome chromosomes. A gain in AZFc region involving only DAZ1 and DAZ4 genes was detected in nine patients and four controls, and was considered as benign. However, changes in AZFc region, that could be related to the oligozoospermia phenotype were detected in three patients. These changes included extensive duplications and deletions involving the four copies of the DAZ gene together with copy number changes affecting other genes. After comparing the selected regions with the literature and with different databases, we suggest that changes such as LOH affecting PLEC, SPATC1, COL1A1, MOV10L1, SYCE3 and ODF3B genes may influence sperm production. Our analysis indicates that, ten out of the twelve miRNAs present in LOH regions could be involved in the infertility phenotype and could have target genes with functions related to spermatogenesis and human reproduction. Additional studies involving gene sequencing and expression analysis are needed to confirm the the correlation between the genotype and oligozoospermia phenotype.
Bockmühl, Ulrike. "Molekularzytogenetische Charakterisierung von Plattenepithelkarzinomen des Kopf-Hals-Bereiches". Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 1999. http://dx.doi.org/10.18452/13706.
Texto completoComparative Genomic Hybridization (CGH) was performed on 100 primary head and neck squamous cell carcinomas, 27 cases of lymph node metastases and 10 second primaries. The main results are summarized as follows: The entity of head and neck squamous cell carcinomas is characterized by a pattern of chromosomal alterations involving deletions chromosomes 3p, 4p/q, 5q, 6q, 8p, 9p, 11p/q, 13q, 18q and 21q combined with overrepresentations of chromosomes 1p, 3q, 5p, 8q, 9q, 11q13, 16p, 17q, 19, 20q and 22q.Well differentiated carcinomas (G1) carry deletions on chromosomes 3p and 9p together with the overrepresentation of 3q indicating early tumor development. Accordingly, the undifferentiated tumors (G3) were charaterized by addtional deletions on chromosomes 4, 5q, 8p, 11, 13q, 18q, 21q and overrepresentations on 8q, 11q13 and 20q suggesting that these changes are preferentially associated with tumor progression.The metastatic phenotype of head and neck suqamous cell carcinomas is significantly associated with deletions of chromosomes 10q and 11.The overall survival time as well as the recurrence free survival time were significantly lower in patients who's tumors showed amplifications of the chromosomal region 11q13 and/or overrepresentations of chromosome 3q (tested for significance by the log rank test p=0.0008 / p=0.0299). Multivariate analysis (Cox's proportional hazards model) revealed both chromosomal alterations as most important independent prognostic factors in HNSCC prior to the established TNM staging system.
Rousseau, Audrey. "Approche diagnostique et pronostique dans les tumeurs gliales : de l'immunohistochimie à l'hybridation génomique comparative". Paris 6, 2007. http://www.theses.fr/2007PA066256.
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