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Bioinformatics analysis of sequences required for localization of RNA during development
Naraine, Ravindra ; Šindelka, Radek (advisor) ; Fulková, Helena (referee) ; Tichý, Boris (referee)
The development of a complex organism from the fusion of two cells (oocyte and sperm) has been a fascinating aspect of developmental biology. It is now known that certain spatially and temporally regulated molecules tightly regulate embryogenesis. The asymmetrical gradient of these molecules within a given cell or within groups of cells helps to guide the differentiation of certain parts of the developing embryo. In fishes and frogs, the establishment of the maternal animal-vegetal transcript gradient within the egg produces the first developmental axis and subsequent formation of the ectoderm, mesoderm, and endoderm regions. Despite this important process, most of our knowledge on this initial animal-vegetal distribution in vertebrates has been limited primarily to the Xenopus laevis model, involved the analysis of only few transcripts and also analyzed only polar regions of the oocyte. This thesis aims to address this deficit in knowledge by leveraging high throughput analysis (RNA sequencing) to characterize and compare the maternal transcriptome and its sub-compartmentalization within the egg of four distantly related models. Additionally, we analyzed different stages of oocyte maturation to determine where the observed localization occurs. The models used were the African clawed frog (Xenopus...
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Analysis of quantitative and qualitative genetic features in the pathogenesis of hereditary solid tumors.
Zemánková, Petra ; Kleibl, Zdeněk (advisor) ; Živný, Jan (referee) ; Tichý, Boris (referee)
Cancer the second most common causes of death in the Czech Republic. Carriers of mutations in genes predisposing to hereditary cancers represent a small but clinically significant group of high risk individuals. Today, dozens of predisposing genes for hereditary tumor syndromes are known and targeted next generation sequencing (NGS) has become a standard approach for their analysis. NGS allows rapid acceleration diagnostics of causal mutation in high-risk individuals. To identify mutations in genes predisposing to hereditary cancers, we designed a panel NGS analysis including subsequent bioinformatics analysis allowing a reliable identification of single nucleotide variants, insertions/deletions, and large intragenic rearrangements. The bioinformatics procedures described in this thesis were used for panel NGS validation, but also for identification of alterations associating with so far undescribed hereditary tumor types. Bioinformatics analyzes have become the basis for the unified processing of large datasets from the CZECANCA consortium and enable the construction of a population-specific database of genotypes that serve to improve clinical diagnostics of cancer predisposition in Czech patients. The versatility of NGS also allows its use for RNA (cDNA-based) analyzes of splicing variants in the...
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Application of whole-exome sequencing methods for the study of rare inherited diseases
Piherová, Lenka ; Kmoch, Stanislav (advisor) ; Sedláček, Zdeněk (referee) ; Tichý, Boris (referee)
Rare diseases (RD) are a heterogeneous group of diseases that affect about 5% of the world population. RDs represent more than 7.000 different phenotypes and many of them are genetically determined. RDs provide unique biological models for understanding the basic principles of molecular and cellular organization and function of human tissues and organs. Results of studies focused at pathogenesis of RDs are often used to diagnose and treat the affected patients. Significant progress in molecular genetic techniques, specifically the use of the next generation sequencing (NGS) in clinical practice, substantially facilitated and improved efficiency of RD laboratory diagnostics. Moreover, these novel testing algorithms identified the previously unknown molecular causes of many RDs. This thesis demonstrates the utility of NGS techniques and bioinformatics processing of obtained data in studies aimed at understanding molecular basis of selected RDs. These methods led to identification and characterization of causative pathogenic variants in the NDUFAF6 and PLD1 genes among patients affected by the Acadian variant of Fanconi disease and patients with a rare congenital heart defect, respectively. This approach was further used to analyze exomes of a large cohort of patients with different types of...
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Analysis of quantitative and qualitative genetic features in the pathogenesis of hereditary solid tumors.
Zemánková, Petra ; Kleibl, Zdeněk (advisor) ; Živný, Jan (referee) ; Tichý, Boris (referee)
Cancer the second most common causes of death in the Czech Republic. Carriers of mutations in genes predisposing to hereditary cancers represent a small but clinically significant group of high risk individuals. Today, dozens of predisposing genes for hereditary tumor syndromes are known and targeted next generation sequencing (NGS) has become a standard approach for their analysis. NGS allows rapid acceleration diagnostics of causal mutation in high-risk individuals. To identify mutations in genes predisposing to hereditary cancers, we designed a panel NGS analysis including subsequent bioinformatics analysis allowing a reliable identification of single nucleotide variants, insertions/deletions, and large intragenic rearrangements. The bioinformatics procedures described in this thesis were used for panel NGS validation, but also for identification of alterations associating with so far undescribed hereditary tumor types. Bioinformatics analyzes have become the basis for the unified processing of large datasets from the CZECANCA consortium and enable the construction of a population-specific database of genotypes that serve to improve clinical diagnostics of cancer predisposition in Czech patients. The versatility of NGS also allows its use for RNA (cDNA-based) analyzes of splicing variants in the...
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