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Detection of β-glucocerebrosidase gene/pseudogene recombination events leading to pathogenic alleles
Peková, Barbora ; Hřebíček, Martin (advisor) ; Schierová, Michaela (referee)
This diploma thesis provides an overview of gene conversion, its role in the pathogenesis of human diseases and the use of methods based on next-generation sequencing (NGS) for detection rare variants of DNA sequence. Labeling of target DNA molecules by random nucleotides in primer and NGS were used for detection point mutations arising de novo in the β-glucocerebrosidase gene by gene conversion between it and its pseudogene in meiotic and mitotic cells of control subjects. Primers specific for the active gene were used to selectively amplify the ninth and tenth exon of the gene where "recombinant" variants occur most frequently. Sequences generated from 20 genomic DNA samples on Illumina MiSeq platform were quality filtered, sorted by unique labels and consensus sequences were created from alignments of sequences carrying the same DNA tag. The number of potential point mutations in the samples ranged between 12 and 48. The mutations were manually re-evaluated from the alignments. The number of alignments with unique labeling was in the range of 7-15 thousand per sample. Only three samples carried possible recombinant mutations, suggesting a lower frequency of conversion in the region than reported by other techniques. Analysis of unique sequences in primer indicated possible ways to improve the...
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Biochemical and molecular studies of the congenital disorders of glycosylation
Ondrušková, Nina ; Hansíková, Hana (advisor) ; Stiborová, Marie (referee) ; Hřebíček, Martin (referee)
Congenital disorders of glycosylation (CDG) represent a rapidly growing group of rare inherited metabolic diseases with estimated prevalence as high as 1:20 000, which are caused by genetic defects that impair the process of glycosylation, i.e. the enzymatic addition of a specific saccharide structure onto a protein or lipid backbone. Due to non-specificity and variability of clinical symptoms in the patients, the medical diagnosis of CDG remains extremely challenging and significantly relies on accurate biochemical and genetic analyses. The overall goal of the present dissertation thesis was to study CDG at the biochemical and molecular genetic level in the context of the Czech and Slovak Republic, which involved three specific aims: A.) to introduce and optimize laboratory screening methods for CDG detection in a group of clinically suspected patients, B.) to determine the corresponding genetic defect in the positive patients selected via CDG screening and to study the pathobiochemical aspects of specific CDG types at the cellular level, and C.) to analyze glycosylation disturbances of non- CDG etiology. Contributions of this work include optimization of isoelectric focusing of apolipoprotein C-III (ApoC-III) as a screening method for O-glycosylation abnormalities, as well as the description of...
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Recombination between the gene and pseudogene for glucocerebrosidase as a mechanism of mutation generation in Gaucher disease
Peková, Barbora ; Hřebíček, Martin (advisor) ; Schierová, Michaela (referee)
Gaucher disease is an autosomal recessive disorder caused by the deficiency of β-glucocerebrosidase. Some Gaucher patients carry in their β-glucocerebrosidase genes complex mutations which apparently arose by a recombination with the non-functional β-glucocerebrosidase pseudogene. Recombination between genes and their corresponding pseudogenes plays a role in the development of other hereditary human diseases. Mutant alleles formed in male and female meiosis are a source of these variations in the gene pool. The study of frequency and scope of recombination events in human disease-associated genes in the gametes is of importance for evaluation of the disease burden in the population. The evaluation of the scope of single recombination events in the β-glucocerebrosidase gene in human gametes is technically challenging. Novel technologies such as next-generation sequencing, nanopore sequencing or droplet digital PCR may have advantages over previously used techniques in this application. Key words: recombination, gene conversion, pseudogene, β-glucocerebrosidase, complex alleles, Gaucher disease
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Molecular basis of X-linked adrenoleukodystrophy: phenotypic variability and skewed X inactivation in heterozygous females
Veselková, Tereza ; Dvořáková, Lenka (advisor) ; Hřebíček, Martin (referee)
X-linked adrenoleukodystrophy (X-ALD) is an inherited peroxisomal disorder caused by mutations in the ABCD1 gene which codes for an ATP binding cassette transporter. As a consequence of these mutations very long chain fatty acids accumulate in cells and patients develop neuronal and adrenal pathologies. There is a broad phenotypic variability in men suffering from X-ALD but the severity of symptoms is independent of ABCD1 genotype. Therefore modifier genes and influence of environmental factors were suggested. Although X-ALD was originally referred to as gonosomal recesive, 88 % of heterozygote women over 60 have neurological symptoms. The association of skewed X chromosome inactivation and severity of disease was studied in several publications with conflicting results. Therefore the penetrance and expressivity of X-ALD in women is probably also influenced by other factors. Based on current knowledge future development of the disease cannot be predicted by evaluation of X inactivation patterns. Key words: X-linked adrenoleukodystrophy, very long chain fatty acids, ABCD1, X inactivation, heterozygotes
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Optimization of newborn screening for cystic fibrosis in the Czech Republic
Krulišová, Veronika ; Macek, Milan (advisor) ; Vrtěl, Radek (referee) ; Hřebíček, Martin (referee)
Newborn screening for cystic fibrosis allows diagnosing patients with cystic fibrosis during asymptomatic stage of their disease or when the symptoms had not fully developed. Due to early diagnosis, patients with cystic fibrosis have the possibility to be treated prior to the occurrence of irreversible changes in the relevant organs, which leads to significantly improved quality of life and patient survival. Commented version of the doctoral thesis presents issues concerning the selection of a suitable newborn screening programme for cystic fibrosis in neonates born in the Czech Republic and establishes requirements for particular analytical and molecular genetics tiers in the tested screening schemes. The aim of this thesis is to nominate newborn screening protocol for cystic fibrosis that leads to optimal parameters in terms of its high sensitivity and specificity, including acceptable costs in the conditions of the Czech Republic health care system. Powered by TCPDF (www.tcpdf.org)
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Characterization of promoter regions of HGSNAT and GBA genes, and a contribution to the study of pathogenesis of MPS IIIC and Gaucher disease
Richtrová, Eva ; Hřebíček, Martin (advisor) ; Macek, Milan (referee) ; Adam, Tomáš (referee)
Pathogenesis of mucopolysaccharidosis type IIIC (MPS IIIC) and Gaucher disease has not been yet fully clarified, and the causes of phenotypical variability between the patients with the same genotype in Gaucher disease remain obscure. Because the variants in the regulatory regions of genes can cause phenotypical differences mentioned above, I have studied promoter regions of HGSNAT and GBA genes mutated in these lysosomal disorders. I have shown that there is an alternative promoter of GBA (P2). Additional studies were aimed to elucidate possible physiological functions of P2, and its possible role in the pathogenesis of Gaucher disease. I have found that P2 is not tissue specific, and that its variants do not influence the variability of phenotype in Gaucher patients with the same genotype. P2 is used differentially neither during the differentiation of monocytes to macrophages nor in macrophages from controls and Gaucher patients, in whom there is a prominent storage only in cells of macrophage origin. We have thus not found any changes that would suggest a role for P2 in the pathogenesis of Gaucher disease. I have characterized the promoter region of HGSNAT and shown that the binding of Sp1 transcription factor is important for its expression. Sequence variants found in HGSNAT promoter in...
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Molecular genetic analysis in Niemann-Pick type C disease
Marešová, Ivona ; Dvořáková, Lenka (advisor) ; Hřebíček, Martin (referee)
Niemann-Pick disease type C (NPC) is a rare, severe disease with autosomal recessive inheritance. Disease is caused by pathogenic mutations located in genes NPC1/NPC2. These genes encode lysosomal non enzymatic NPC1/NPC2 proteins that are part of lipid transport. As a result of malfunction of these proteins intracellular accumulation of lipids occurs, in particular free cholesterol and glycolipids. Causal therapy is currently still unsatisfactory therefore new therapies are evolved. However these therapies depend on whether the patient cells contain at least residual amount of transcript NPC1 gene. In a group of patiens, for which a fibroblast culture was available, I analyzed the effect of pathogenic mutations on the expression level of the transcript. Results showed that for all pathogenic mutations transcript level is low, but detectable. Moreover, I characterized the structure of the NPC1 gene promoter. By sequence analysis I found polymorphisms rs8099071, rs28403610, rs2981422, rs1652354, rs1788774, rs1788772 in promoter. On the basis of the composition of polymorphisms in individual patiens, I estimate six different haplotypes. I performed mutation analysis in DNA of recently diagnosed patient. I found only one pathogenic mutation p.I1061T (c.3182T> C) in the NPC1 gene. Therefore I tested...
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