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Application of novel genomic techniques in studies of pathogenesis of selected rare inherited disorders
Nosková, Lenka ; Kmoch, Stanislav (advisor) ; Sedláček, Zdeněk (referee) ; Živný, Jan (referee)
Rare diseases are a heterogeneous group of disorders. Knowledge of their molecular basis is poor and till recently there were no appropriate methodical approaches due to a limited number of patients. Novel genomic techniques, especially the DNA array technology and the next generation sequencing emerging in last few years, enabled studies of these diseases even in small families and sporadic cases. This PhD thesis focuses on application of novel genomic techniques in studies of rare inherited diseases. It describes a use of DNA array technology in linkage analysis, analysis of differential gene expression, analysis of copy number variations and homozygous mapping, and a use of next generation sequencing technology. Combination of these methods was used for identification of molecular basis of adult neuronal ceroid lipofuscinosis, Rotor syndrome, isolated defect of ATP synthase and mucopolysaccharidosis type IIIC.
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Characterization of Mitochondrial Respiratory Chain Defects Using DNA Microarrays
Čížková, Alena ; Kmoch, Stanislav (advisor) ; Kováč, Ladislav (referee) ; Červinková, Zuzana (referee)
A mitochondrion is a organelle under nuclear and mitochondrial genetic control and its maintence requires a nucleo-mitochnodrial cross-talk. Better understanding of mitochondrial pahologies using various gene expression techniques. This thesis presents the implementation and application of microarray technology for identification of disease causing genes in respiratory chain disorders, expecially in patients with ATP synthase deficiency of nuclear origin. The introduction to this thesis provides an overview of mitochondrial structure and biogenesis, respiratory chain complexes and their disorders as well as different types of microarrays. A study of mitochondrial ATP synthase deficiency represents the major experimental part of this thesis and is accordingly that were used in further studies centered on characterization of inherited metabolic disorders. This is documented in positional cloning of patientes with lysosomal storage disorders - mucopolysaccharidosis IIIC.
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Molecular Basis of Hereditary Hyperuricaemic Nephropathies
Vyleťal, Petr ; Kmoch, Stanislav (advisor) ; Viklický, Ondřej (referee) ; Jirsa, Milan (referee)
Familial juvenile hyperuricemic nephropathy (FJHN) and medullary cystic kidney disease type 1 (MCKD1) and type 2 (MCKD2) are autosomal dominant tubulointerstitial nephropathies characterized by combinations of hyperuricaemia, gouty arthritis, progressive renal insufficiency, and in some but not all families, medullary cysts. The phenotypic expression of these diseases is inconsistent, overlaps and indicates broader genetic and allelic heterogeneity. Their pathophysiology was mainly unknown. Previous studies localized FJHN/MCKD genes to chromosomes 16p11 and 1q21. This thesis was primarily aimed at identification of molecular bases and mechanisms underlying FJHN/MCKD. To follow this aim, we focused on collection and characterization of FJHN/MCKD patients and families, identification of disease causing genes in affected families, characterisation of identified proteins and their mutated forms and the isolation and characterisation of interacting partners of newly identified proteins. We employed and established numerous molecular genetic, molecular biological and biochemical methods. We gathered one of the largest sets of families with FJHN/MCKD in the world. In about 26% of families we identified UMOD (uromodulin encoding) gene mutations and characterised by various approaches 6 uromodulin mutant proteins....
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Molecular Basis of Familial Hyperuricemic Nephropathies
Živná, Martina ; Kmoch, Stanislav (advisor) ; Jirsa, Milan (referee) ; Sedláček, Zdeněk (referee)
In 1960 Duncan and Dixon described family whth chronic tubulointerstitial kidney disease associated with juvenile onset of hyperuricemia and gout. Based on combination of these clinical symptoms they named the disease familial juvenile hyperuricemic nephropathy (FJHN) [1]. Disease with very similar clinical presentation but different age of onset and kidney histology was described as a medullary cystic kidney disease (MCKD) in 1977 [2]. Until recently the molecular basis and pathogenesis of this syndrome remained unknown. The long term aim of our research group is to elucidate the genetic basis of the disease and to solve pathogenetic mechanisms leading to the individual clinical and biochemical symptoms (e.g. hyperuricemia) and kidney damage in general. We systematically identify patients with this disease and healthy family members and collect relevant clinical information and samples for classification (urine, blood, tissue biopsies) and subsequent clinical, biochemical, molecular biology and cell pathology correlations. We [3, 4] and others [5-7] proved genetic heterogeneity of FJHN and defined four FJHN loci on chromosomes 1q21, 1q41, 16p11.2. and 17q21.3. Further research defined disease causing mutations in three genes - uromodulin (UMOD) [8], hepatonuclear factor 1-beta (HNF-1) [9] and renin (REN)...
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Molecular analysis in cases of inherited diseas
Mrázová, Lenka ; Kmoch, Stanislav (advisor) ; Jirsa, Milan (referee) ; Macek, Milan (referee)
Urcení vztahu mezi onemocnením a jeho molekulární podstatou je jedním z hlavních cílu lékarské genetiky. V rámci studie: "Molekulární analýza vybraných dedicne podmínených onemocnení" byly popsány postupy, které vedou k objasnení molekulární podstaty u onemocnení s již známými odpovednými geny i u onemocnení, u kterého byl odpovedný gen teprve identifikován. Studie prispela k rozšírení znalostí zkoumaných dedicných onemocnení. Zavedené postupy molekulárních analýz jsou soucástí diagnostiky na Ústavu dedicných metabolických poruch v Praze. Výsledky techto analýz slouží k prevenci, prognóze i lécbe onemocnení a u postižených rodin byla umožnena prenatální diagnostika. Výsledky byly publikovány v nekolika domácích i zahranicních odborných casopisech a prezentovány na mezinárodních konferencích. Nekteré z publikací byly dále citovány.
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Genetic and molecular basis of neurodegenerative and neuropsychiatric diseases
Jedličková, Ivana ; Kmoch, Stanislav (advisor) ; Fajkusová, Lenka (referee) ; Laššuthová, Petra (referee)
Next-generation (NGS) and third-generation (TGS) sequencing methods have played a key role in strategies of disease genes identification. Especially the exome sequencing increased the efficiency of causal variants identification up to tens of percent in study cohorts. Rare neurodegenerative diseases are clinically and genetically heterogeneous and show a broad differential diagnostics. NGS and TGS technologies have been crucial in our understanding of the pathomechanism of rare neurodegenerative diseases. NGS and TGS, used by research laboratories, have been essential for many patients to determine a correct diagnosis, provide genetic counselling and reach an adequate treatment. This thesis focuses on molecular mechanisms of selected rare neurodegenerative diseases, namely adult neuronal ceroid lipofuscinosis (ANCL), spinal muscular atrophy (SMA) and neuronal intranuclear inclusion disease (NIID). Modern DNA sequencing methods led to identification of causal lesions in ANCL suspect patients. We provide a concept of genetic testing for SMN1 negative SMA patients and present a method for validation of tandem repeat expansion in NIID. Key words: adult neuronal ceroid lipofuscinosis, spinal muscular atrophy, neuronal intranuclear inclusion disease, next-generation sequencing methods, DNAJC5
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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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Current methods of genome analysis and their use in identification of genetic determinants of human diseases
Stránecký, Viktor ; Kmoch, Stanislav (advisor) ; Kleibl, Zdeněk (referee) ; Pačes, Jan (referee)
The study of rare genetic diseases presents unique opportunity to uncover the genetic and molecular basis of human traits and greatly helped to the identification of genes, to the elucidation of their function and to the characterization of metabolic pathways and cellular processes. Over the past decades, linkage analysis has been appropriate approach to search for the genes causing Mendelian diseases and contributed to the identification of many genes, but the genetic cause of many diseases remains unknown. New methods of studying the human genome, microarray technology and massively parallel sequencing (next generation sequencing), represent a way to efficiently identify the cause of genetically determined diseases, based on direct observation of mutations in the genome of affected individuals. These techniques replaced the traditional method of disease gene identification represented by linkage analysis and sequencing of candidate genes and have become the standard approach to elucidate the molecular basis of diseases. In this work, i describe the the results achieved by using these methods - identification of the genes underlying mucopolysacharidosis type IIIC, isolated defect of ATP synthase, Rotor syndrome, autosomal dominat ANCL and GAPO syndrome.
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