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CNV detection in the sequencing data
Pleskačová, Barbora ; Škutková, Helena (referee) ; Jugas, Robin (advisor)
Copy number variation detection in prokaryotic organisms is currently receiving more and more attention, mainly due to the association of CNV with pathogenicity and antibiotic resistance in bacteria. The algorithm designed in this thesis uses peak detection in sequencing coverage to detect CNV segments. Read coverage is commonly obtained by mapping sequencing reads of one individual to an already known reference of another individual of the same species. However, two individuals will always differ in a certain number of genes, resulting in unmapped reads that are unnecessarily discarded. Therefore, this work assumes that the biological accuracy of CNV detection can be increased by using a new reference that is created from the same set of reads as the reads mapped to this reference. Sequencing reads of Klebsiella pneumoniae individuals are used to verify this assertion.
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CNV detection in bacterial genomes
Lacinová, Michaela ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
This master thesis deals with analysis of structural variation of genome and with methods of its sequencing across all generations. Subsequently it contains a description of copy number variation and methods of its detection. The experimental part focuses on algorithm proposal for CNV detection according analysis and testing of uneven coverage in genome, variable representation of GC content and distance of sequence reads. Finally, the algorithm for detecting copy number variation is tested on genomic data of bacteria Klebsiella pneumoniae.
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Cryptic Rearrangements of Human Chromosomes Associated with Autism Spectrum Disorders
Křivánková, Anna ; Šolc, Roman (advisor) ; Růžičková, Šárka (referee)
Autism spectrum disorders (ASD) are heterogeneous group of neurodevelopmental disabilities characterized by antisociality and atypical behavioral patterns. Its etiology is very complex, autism is usually formed by combining many factors. One of the causes may be genetic (gene mutation). It is known about 450 candidate genes for ASD so far. Minority of these genes occur in loci which are affected by cryptic rearrangements. These rearrangements significantly contribute to manifestation of this disorder. Patologies they cause, lead to syndromes with high penetrance for ASD such as Angelman/Prader-Willi or DiGeorge syndrome. Other loci are found on chromosome 1, 2 or 16. Due to short time of studies of cryptic rearrangements, phenotypic variability and number of patients we can expect more researches in the future. These researches are expected not to overlook the impact of the aberrations on formation of autism spectrum disorders.
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CNV detection in the sequencing data
Pleskačová, Barbora ; Škutková, Helena (referee) ; Jugas, Robin (advisor)
Copy number variation detection in prokaryotic organisms is currently receiving more and more attention, mainly due to the association of CNV with pathogenicity and antibiotic resistance in bacteria. The algorithm designed in this thesis uses peak detection in sequencing coverage to detect CNV segments. Read coverage is commonly obtained by mapping sequencing reads of one individual to an already known reference of another individual of the same species. However, two individuals will always differ in a certain number of genes, resulting in unmapped reads that are unnecessarily discarded. Therefore, this work assumes that the biological accuracy of CNV detection can be increased by using a new reference that is created from the same set of reads as the reads mapped to this reference. Sequencing reads of Klebsiella pneumoniae individuals are used to verify this assertion.
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CNV detection in bacterial genomes
Lacinová, Michaela ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
This master thesis deals with analysis of structural variation of genome and with methods of its sequencing across all generations. Subsequently it contains a description of copy number variation and methods of its detection. The experimental part focuses on algorithm proposal for CNV detection according analysis and testing of uneven coverage in genome, variable representation of GC content and distance of sequence reads. Finally, the algorithm for detecting copy number variation is tested on genomic data of bacteria Klebsiella pneumoniae.
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Cryptic Rearrangements of Human Chromosomes Associated with Schizophrenia
Jurišová, Lívia ; Šolc, Roman (advisor) ; Brynychová, Iva (referee)
Schizophrenia is a severe mental disorder with high heritability and complex genetics which interacts with environmental factors and leads to a wide range of symptoms. The emergence of modern cytogenetic and molecular genetic techniques has allowed uncovering one of the po- ssible causes - cryptic chromosomal rearrangements. The size of rearrangements, also known as microdeletions and microduplications, is under 3-5 Mb. Aberrations may affect multiple genes and their gene dosage. The research of cryptic rearrangements in association with schizophrenia began in 2008 with the identification of three pathogenic aberrations. Over time studies have identified more cryptic rearrangements and new studies supporting or not supporting their role in the disorder have been published. Research of the candidate genes and their possible interac- tions has also been conducted. It is hypothesized that schizophrenia is caused by pathologically changed brain connectivity, in which the changed gene dosage by cryptic rearrangements may play a role. The research is in its beginnings, and we can expect the identification of new rear- rangements. Further research may lead to a better understanding of the origin and symptoms of schizophrenia, and play a role in prenatal diagnostics and treatment. Key words: cryptic...
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Cryptic Rearrangements of Human Chromosomes Associated with Autism Spectrum Disorders
Křivánková, Anna ; Šolc, Roman (advisor) ; Růžičková, Šárka (referee)
Autism spectrum disorders (ASD) are heterogeneous group of neurodevelopmental disabilities characterized by antisociality and atypical behavioral patterns. Its etiology is very complex, autism is usually formed by combining many factors. One of the causes may be genetic (gene mutation). It is known about 450 candidate genes for ASD so far. Minority of these genes occur in loci which are affected by cryptic rearrangements. These rearrangements significantly contribute to manifestation of this disorder. Patologies they cause, lead to syndromes with high penetrance for ASD such as Angelman/Prader-Willi or DiGeorge syndrome. Other loci are found on chromosome 1, 2 or 16. Due to short time of studies of cryptic rearrangements, phenotypic variability and number of patients we can expect more researches in the future. These researches are expected not to overlook the impact of the aberrations on formation of autism spectrum disorders.
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