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Localization of Methylation Sites in Transposons
Kmeť, Miroslav ; Martínek, Tomáš (referee) ; Vogel, Ivan (advisor)
This master's thesis deals with the creation of a tool for the extraction of methylation level from transposon sequences. Transposons are DNA elements with ability to move or copy themselves and their activity is regulated by DNA methylation. Sequence methylation information is stored in the bisulfite data and their processing is done with parts of two existing tools in a combination with implemented modules. Created tool takes into consideration unique challenges brought in the methylation calling process by transposable elements and it's functionality is presented on a set of experiments with simulated and real data.
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Advanced Computational Methods for CNV Detection in Bacterial Genomes
Jugas, Robin ; Bystrý, Vojtěch (referee) ; Šafránek,, David (referee) ; Vítková, Helena (advisor)
Hlavní pozornost v oblasti strukturálních variací je zaměřena na lidské genomy. Detekce změny variace počtu kopií (CNV) u bakterií je tedy méně rozvinutou oblastí. Běžně používané metody detekce CNV neberou v úvahu specifika bakteriálních kruhových genomů a obecně existuje prostor pro zlepšení metrik výkonnosti. Tato práce představuje metodu detekce CNV nazvanou CNproScan zaměřenou na bakteriální genomy. CNproScan implementuje hybridní přístup kombinující signály hloubky čtení a párů čtení. Bere v potaz všechny vlastnosti bakterií a využívá pouze sekvenační data. Na základě výsledků ze srovnání dosáhl CNproScan velmi dobrých výsledků v různých podmínkách. Pomocí informací z párových čtení jsou CNV klasifikovány do několika kategorií. Ve srovnání s jinými metodami může CNproScan také detekovat mnohem kratší CNV. Vzhledem k nutnosti slučovat nejen signály různých přístupů, ale také výsledky různých algoritmů, dizertační práce také představuje pipelinu nazvanou ProcaryaSV vyvinutou k detekci CNV s využitim pěti nástrojů a slučování jejich výsledků. ProcaryaSV se stará o celý postup od kontroly kvality čtení, ořezávání konců čtení, zarovnání čtení až k detekci CNV.
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Processing of Unique Molecular Identifiers without Mapping to a Reference Genome
Barilíková, Lujza ; Demko, Martin (referee) ; Sedlář, Karel (advisor)
Hlavným cieľom tejto práce je návrh nového algoritmu k spracovaniu unikátnych molekulárnych indexov bez mapovania na referenčný genóm. O tieto náhodné oligonukleotidové sekvencie neustále vzrastá záujem, pretože uľahčujú rozpoznávať PCR chyby a skresľovanie údajov. Keďže používanie technológií sekvenovania novej generácie neustále rastie, je vynaložené veľké úsilie vyvíjať nástroje pre analýzu produkovaných dát. V súčasnosti sú nástroje na riešenie týchto chýb relatívne časovo náročné a zložité z dôvodu výpočtovo náročného zarovnania. Najdôležitejšie obmedzenie týchto nástrojov spočíva v skutočnosti, že pri spracovávaní duplikátov sú povolené multi-mapované čítania. Tieto čítania sú zvyčajne ignorované, čo môže viesť k zníženiu kvantitatívnej presnosti a spôsobiť zavádzajúcu interpretáciu výsledkov daného sekvenovania. V snahe vyriešiť tento problém je v tejto práci uvedený nový prístup, ktorý umožňuje odhad absolútneho počtu jedinečných molekúl s relatívne rýchlym a spoľahlivým spôsobom.
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Classification of Small Noncoding RNAs
Žigárdi, Tomáš ; Martínek, Tomáš (referee) ; Vogel, Ivan (advisor)
This masters's thesis contains description of designed and implemented tool for classification of plant microRNA without genome. Properties of mature and star sequences in microRNA duplexes are used. Implemented method is based on clustering of RNA sequences (with CD-HIT) to mainly reduce their count. Selected representants from each clusters are classified using support vector machine. Performance of classification is more than 96% (based on cross-validation method using the training data).
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Detection of chimeras in amplicon sequencing
Heřmánková, Kristýna ; Jurečková, Kateřina (referee) ; Sedlář, Karel (advisor)
Chimeric sequences are the most common artifacts that can occur in sequencing data after the sample amplification using the polymerase chain reaction. The presence of these artifacts can negatively affect results of the analysis. Therefore, the detection and subsequent filtration of chimeric sequences is an important step in the computational processing of sequencing data. This work deals with the principle of chimera formation and the possibility of reducing their occurrence. The aim of this work is to implement an algorithm for chimeras detection in R language and testing its accuracy on data provided by the Veterinary Research Institute in Brno.
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Optimization of the Next-Generation Sequencing Data Alignment
Šalanda, Vojtěch ; Bendl, Jaroslav (referee) ; Vogel, Ivan (advisor)
This thesis presents short DNA alignment tools optimization. These short DNA reads are products of next\nobreakdash-generation sequencing technologies. The results produced by existing align\-ment tools can be influenced by various parameters. For this purpose, an optimization framework to find the optimal values of selected parameters was developed. This framework is based on differencial evolution algorithm and its main goal is to maximize the alignment accuracy. The functionality of the framework was tested on both real and generated data sets of short DNA reads. An accurate alignment is crucial for correct prediction of various genetic characteristics.
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Developmental disorders of the lens and anterior segment of the eye
Jedličková, Jana ; Ďuďáková, Ľubica (advisor) ; Šafka Brožková, Dana (referee) ; Cvekl, Ales (referee)
The anterior segment of the eye includes the eyelids, eyelashes, tear film, cornea, conjunctiva, iris, pupil, ciliary body, chamber angle, and lens. Cataracts and anterior segment dysgenesis are a highly heterogeneous group of diseases exhibiting all types of Mendelian inheritance. The aim of this thesis was molecular genetic analysis of 51 patients from 23 families with congenital and early onset cataracts and/or anterior segment dysgenesis, using a modern as well as conventional methods, such as next-generation sequencing, direct sequencing, bioinformatic and functional analyses including the use of artificial splicing vectors. We identified 24 causal variants in the coding, non-coding and regulatory regions of the PAX6, FTL, FOXC1, PITX2, FOXE3, and CHRDL1 genes. We confirmed the role of the n.37C>T variant in MIR204 in the development of chorioretinal dystrophy variably associated with iris coloboma, early-onset cataracts and congenital glaucoma. Splicing assay confirmed pathogenic effect of two mutations on pre-mRNA splicing of the PAX6 gene. Establishing molecular genetics diagnosis improves patient counselling and their relatives in terms of the prognosis and risk of developing secondary glaucoma Key words: molecular-genetic diagnosis, anterior segment dysgenesis, next-generation sequencing,...
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Molecular genetic analysis of rare ocular disorders in Roma population from the Czech Republic
Rysková, Natálie ; Lišková, Petra (advisor) ; Klímová, Aneta (referee)
The Roma are the largest and most widespread transnational ethnic community. The Czech Republic estimates their 2% representation in its population. Due to the high level of endogamy, the spectrum and frequency of hereditary diseases in the Roma population differ from the majority population. Hereditary eye diseases are one of the most common causes of blindness in younger adults and thus represent a real socio-economic burden. The aim of the thesis was to perform molecular genetic analysis in individuals of Roma origin suffering from hereditary diseases affecting vision, including dual impairments and syndromes, and to determinate the frequency of the detected pathogenic variants in this population. Molecular genetic analysis of 17 families was performed using direct and whole exome sequencing. Within the framework of an international collaboration, the degree of their mutual kinship was calculated using the PLINK program. The frequency of selected variants was determined in a control dataset comprising 156 Roma exomes and genomes. The spectrum of analyzed diseases included various retinal dystrophies, primary congenital glaucoma, Usher syndrome, neuronal ceroid lipofuscinosis, Noonan syndrome, nanophthalmos and congenital cataract, facial dysmorphism and neuropathy. The results of the thesis...
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Identification of hereditary factors influencing the formation of a pancreatic carcinoma and other solid tumours
Král, Jan ; Janatová, Markéta (advisor) ; Hojný, Jan (referee) ; Šeborová, Karolína (referee)
Pancreatic adenocarcinoma (PDAC) has one of the worst prognoses out of all cancers worldwide. Endometrial carcinoma (EC) is the most common gynecological cancer. Genetic background of tumors is highly heterogenous and differs among populations. We have analyzed DNA of 226 PDAC patients and 527 EC patients using panel next- generation sequencing. Targeted genes were divided into main predisposition genes (11 for PDAC, 19 for EC) and other candidate genes. EC patients were categorized based on meeting the indication criteria for germline genetic testing. Two sets of population-matched controls were used (controls with negative cancer history, and general population controls). Germline pathogenic variants (PV) in main predisposition genes were identified in 18 (8.0%) PDAC patients. The most mutated gene was BRCA2 (50% of carriers). PDAC risk was significantly elevated in carriers of PV in BRCA1 (OR = 10.4, p = 0.04), BRCA2 (OR = 6.4, p = 0.0009), and CHEK2 (OR = 17.5, p = 0.003). Germline mutations in genes participating in homologous recombination processes were associated with improved overall survival of patients. Among EC patients there were 60 (11.4%) carriers of PV in main predisposition genes. Carriers of PV in Lynch syndrome (LS) genes had markedly elevated risk of developing EC (OR = 22.4, p...
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qPCR diagnostika střevního prvoka \kur{Blastocystis} sp. v souboru vzorků od zdravých lidí
ŠLOUFOVÁ, Martina
The main aim of this study was to introduce and optimize the qPCR diagnostic protocol for detection of intestinal protist, Blastocystis sp. We compared the sensitivity of conventional PCR (cPCR) and real-time PCR (qPCR) in a set of 288 human samples from gut-healthy individuals and subtype diversity as detected by Next-generation sequencing (NGS) versus Sanger sequencing. The overall prevalence of Blastocystis sp. was 29 %. Based on the results, we found out that qPCR is a more sensitive method than cPCR. In subtype detection, NGS was completely in agreement with Sanger sequencing but showed higher sensitivity for mixed subtype colonization within one host. A combination of these two approaches could be beneficial for future epidemiological studies.
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