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Analysis of copy number variant (CNV) in genomes of patiens with mental retardation
Hančárová, Miroslava ; Sedláček, Zdeněk (advisor) ; Gaillyová, Renata (referee) ; Michalová, Kyra (referee)
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...
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Brain Tumor Cells Genome Instability. Correlation of clinial, morphological and molecular-cytogenetic data
Kramář, Filip ; Michalová, Kyra (advisor) ; Minárik, Marek (referee) ; Novák, Zdeněk (referee)
Gliomas are brain tumors arising from neuroglia. In most cases astrocytic or oligodendroglial component is the main element of the tumor. Non-random chromosomal abberations are found in tumor cells as was revealed previously. The aim of this study was a fluorescence in-situ hybridisation analysis (FISH) of tissue samples obtained during neurosurgical procedures, determine the frequence of selected chromosomal abberations, further correlation with morphological and clinical data and statistical analysis of the results. During six years 264 tissue samples were gained in which FISH with defined probes was performed. The acquired results were compared with histological analysis and selected clinical data (age, Karnofsky score, extent of resection, overall survival). The whole series was divided into 7 groups by tumor type for further statistical analysis. In every group median and mean survival time was calculated, Kaplan-Meier analysis was focused on influence of selected parameters to overall survival. In some categories Cox regression model was created to achieve a hazard ratio of selected parameters. In WHO Grade II and III tumors the risk of malignant progression and tumor upgrading is significantly higher in comparison with samples where specific abberations were not found (EGFR amplification, CDKN2A and...
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Analysis of structural chromosomal rearrangements in hematological neoplasias; Study of structural chromosomal rearrangements of cells of chronic lymphocytic leukemia after DSP30/IL2 stimulated cultivation
Hrubá, Martina ; Michalová, Kyra (advisor) ; Goetz, Petr (referee) ; Březinová, Jana (referee)
Cytogenetic analysis of cells of chronic lymphocytic leukemia (CLL) is difficult because of their low proliferative activity. To obtain sufficient number of mitoses for performing chromosomal analysis a suitable stimulation of cell division is needed. Using DSP30/IL2 stimulated cultivation 391 CLL samples were investigated in 5 years' period. The cultivation was showed to have high success rate (96%; 375/391) with also high rate of detection of pathological clones by both karyotype and metaphase FISH analyses (in 84% of samples; 329/391). Almost in half of samples (44%; 171/391) other aberrations than recurrent FISH (i.e. 13q14 deletion, trisomy 12, TP53, ATM genes deletions) were found. Also high frequency of translocations (37%; 144/391), complex karyotypes (28%; 111/391) and clonal evolution, which was detected in one third of all samples (34% of samples with presence of more than two clones; 133/391) and like a new event in disease duration even more frequently (in 39% of samples repeatedly investigated after stimulated cultivation; 21/54), was revealed. The presence of translocations, complex karyotypes and clonal evolution was associated with progressive form of disease (P 0,000003, resp. P 0,0002 and P 0,05/P 0,04). In cases of the recurrent deletions the detailed analysis of metaphase...
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Detection of submicroscopic chromosomal aberrations in phenotypically abnormal carriers of apparently balanced rearrangements using array CGH
Slámová, Zuzana ; Sedláček, Zdeněk (advisor) ; Michalová, Kyra (referee) ; Kuglík, Petr (referee)
Carriers of apparently balanced chromosomal aberrations (BCA) are usually phenotypically normal. However, it has been estimated that up to 27% of these BCA may be associated with an abnormal phenotype, most often caused by cryptic imbalances at the breakpoints, gene disruption by the breakpoint or via the position effect. In contrast to conventional karyotyping, molecular cytogenetic techniques enable more detailed BCA characterization and better correlation between genotype and phenotype of the patient. The aim of this thesis was to evaluate the presence of copy number variants (CNVs) at breakpoints or elsewhere in the genome in patients with abnormal phenotype who carry de novo or inherited BCA. 54 BCA were investigated using array CGH (20 de novo cases, 27 inherited and 7 cases of unknown origin) including 32 reciprocal translocations, 6 robertsonian translocations, 12 inversions and 4 complex chromosomal rearrangements. If possible, the parents were also examined to ascertain the inheritance of the relevant CNVs. In order to specify microarray findings or exclude gene disruption, FISH was used in selected patients. Among the patients included, in 31,5% (17/54) at least one (in 8 patients more than one) significant CNV was detected. Four cases carried cryptic imbalances only at the breakpoints,...
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Analysis of copy number variant (CNV) in genomes of patiens with mental retardation
Hančárová, Miroslava ; Sedláček, Zdeněk (advisor) ; Gaillyová, Renata (referee) ; Michalová, Kyra (referee)
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...
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Analysis of structural chromosomal rearrangements in hematological neoplasias; Study of structural chromosomal rearrangements of cells of chronic lymphocytic leukemia after DSP30/IL2 stimulated cultivation
Hrubá, Martina ; Michalová, Kyra (advisor) ; Goetz, Petr (referee) ; Březinová, Jana (referee)
Cytogenetic analysis of cells of chronic lymphocytic leukemia (CLL) is difficult because of their low proliferative activity. To obtain sufficient number of mitoses for performing chromosomal analysis a suitable stimulation of cell division is needed. Using DSP30/IL2 stimulated cultivation 391 CLL samples were investigated in 5 years' period. The cultivation was showed to have high success rate (96%; 375/391) with also high rate of detection of pathological clones by both karyotype and metaphase FISH analyses (in 84% of samples; 329/391). Almost in half of samples (44%; 171/391) other aberrations than recurrent FISH (i.e. 13q14 deletion, trisomy 12, TP53, ATM genes deletions) were found. Also high frequency of translocations (37%; 144/391), complex karyotypes (28%; 111/391) and clonal evolution, which was detected in one third of all samples (34% of samples with presence of more than two clones; 133/391) and like a new event in disease duration even more frequently (in 39% of samples repeatedly investigated after stimulated cultivation; 21/54), was revealed. The presence of translocations, complex karyotypes and clonal evolution was associated with progressive form of disease (P 0,000003, resp. P 0,0002 and P 0,05/P 0,04). In cases of the recurrent deletions the detailed analysis of metaphase...
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Brain Tumor Cells Genome Instability. Correlation of clinial, morphological and molecular-cytogenetic data
Kramář, Filip ; Michalová, Kyra (advisor) ; Minárik, Marek (referee) ; Novák, Zdeněk (referee)
Gliomas are brain tumors arising from neuroglia. In most cases astrocytic or oligodendroglial component is the main element of the tumor. Non-random chromosomal abberations are found in tumor cells as was revealed previously. The aim of this study was a fluorescence in-situ hybridisation analysis (FISH) of tissue samples obtained during neurosurgical procedures, determine the frequence of selected chromosomal abberations, further correlation with morphological and clinical data and statistical analysis of the results. During six years 264 tissue samples were gained in which FISH with defined probes was performed. The acquired results were compared with histological analysis and selected clinical data (age, Karnofsky score, extent of resection, overall survival). The whole series was divided into 7 groups by tumor type for further statistical analysis. In every group median and mean survival time was calculated, Kaplan-Meier analysis was focused on influence of selected parameters to overall survival. In some categories Cox regression model was created to achieve a hazard ratio of selected parameters. In WHO Grade II and III tumors the risk of malignant progression and tumor upgrading is significantly higher in comparison with samples where specific abberations were not found (EGFR amplification, CDKN2A and...
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Analysis of complex chromosomal rearrangements in tumor cells and their impact on pathogenesis and prognosis of malignant diseases
Lizcová, Libuše ; Michalová, Kyra (advisor) ; Goetz, Petr (referee) ; Kuglík, Petr (referee)
Cytogenetic abnormalities are characteristic attribute of cancer cells. To date, clonal chromosomal aberrations have been found in majority of tumors and they represent important part of management of patients with malignant diseases. Using modern molecular cytogenetic methods (I-FISH, mFISH, mBAND, CGH, aCGH, SNP array) we performed precise analysis of complex chromosomal rearrangements (CCR) in patients with various hematological malignancies and difuse gliomas. We described particular aberrations in detail and found chromosomes and chromosomal parts which were involved in CCR most frequently. We determined recurrent chromosomal breakpoints and pointed out to regions with important role in initiation and progression of the disease. From the clinical point of view, we proved that complex chromosomal aberrations found at the time of diagnosis are poor prognostic factor. In our cohorts of patients, complex chromosomal rearrangements were associated with resistance to treatment, higher occurrence of relapses and shorter overall survival. Results of our study proved significance of molecular cytogenetic analysis not only for diagnosis and prognosis of patients with different types of tumors but also for clarification of mechanisms leading to malignant transformation of the cell. Detailed chromosomal...
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název v anglickém jazyce není uveden
Stopková, Pavla ; Zvolský, Petr (advisor) ; Martásek, Pavel (referee) ; Michalová, Kyra (referee)
Psychiatric illnesses represent a substantial part of civilization diseases and their frequency is rising. Depressive episode and alcohol addiction are among the 10 most serious conditions of our time. Epidemiological studies show that every year 100 million people worldwide will suffer depression. At one stage in our lifetime 17% of us will go through a depressive episode. According to Scheene, psychiatric day hospitals fulfil four major tasks: (Scheene, A. H. et al, 1988): They are an alternative to classical psychiatric inpatient care They follow after classical psychiatric inpatient care They are an intensive form of outpatient care They are used for long term rehabilitation of patients with chronic psychiatric disorder One of the major shortcomings of psychiatric day hospital research is the fact that over the last two decades particularly, a broad variety of conceptual models have proliferated through the whole of Europe and the US. They range from crisis intervention and drop-in centres to long term rehabilitative services or highly specialized day centres and there are not many surveys being carried out to assess the detailed characteristics of these services. Therefore the research focuses mainly on comparing acute psychiatric day care with traditional inpatient treatment. Systematic...
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Dipeptidyl Peptidase-IV Activity and/or Structure Homologues : Their Role in Gliomagenesis
Stremeňová, Jarmila ; Šedo, Aleksi (advisor) ; Michalová, Kyra (referee) ; Mandys, Václav (referee)
Dipeptidyl peptidase-IV (DPP-IV, EC 3.4.14.5) together with fibroblast activation protein-alpha (FAP), DPP-7, -8 and -9 belong to the functionally defined group of "DPP-IV activity and/or structure homologues" (DASH). They hydrolyse N-terminal X-Pro dipeptides from a number of biologically active peptides like neuropeptide Y, substance P and chemokines such as stromal cell derived factor-1alpha (SDF-1). Limited proteolysis of such mediators by DPP-IV-like enzymatic activity can modify consequent biological responses of the target cells. By that, DASH molecules are supposed to be important for multiple cellular processes, including cell proliferation, malignant transformation, migration and invasion and thus involved in cancer development and progression. This study was set up to characterise DASH expression pattern and DPP-IV-like enzymatic activity in human astrocytic tumours in comparison with non-tumorous brain tissue, and to assess its context with the expression of receptors of some local mediators- DASH substrates implicated in gliomagenesis. Moreover, the possible functional relevance of DASH molecules in growth properties of transformed astrocytic cells was studied in model of primary cell cultures derived from the glioblastoma in vitro. (...) Hence we speculate that although the upregulated DPP-IV...
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