Mon projet de doctorat était de créer un pipeline pour taxono-génomique pour la comparaison de plusieurs génomes bactériens. Deuxièmement, je automatisé le processus d'assemblage (NGS) et annotation à l'aide de divers logiciels open source ainsi que la création de scripts de maison pour le laboratoire. Enfin, nous avons intégré le pipeline dans la description de plusieurs espèces bactériennes de laboratoire sur. Cette thèse est divisée principalement en Taxono- génomique et Microbiogenomics. Les avis de la section taxono-génomique, décrit sur les avancées technologiques en génomique et métagénomique pertinentes dans le domaine de la microbiologie médicale et décrit la stratégie taxono-génomique en détail et comment la stratégie polyphasique avec des approches génomiques sont reformatage de la définition de la taxonomie bactérienne. Les articles décrivent les bactéries cliniquement importantes, leur séquençage complet du génome et les études génomiques comparatives, génomiques et taxono-génomique de ces bactéries. Dans cette thèse, j'ai inclus les articles décrivant ces organismes: Megasphaera massiliensis, Corynebacterium ihumii, Collinsella massiliensis, Clostridium dakarense. Bacillus dielmoensis, jeddahense, Occidentia Massiliensis, Necropsobacter rosorum et Pantoea septica. Oceanobacillus / My PhD project was to create a pipeline for taxono-genomics for the comparison of multiple bacterial genomes. Secondly I automated the process of assembly (NGS) and annotation using various open source softwares as well as creating in house scripts for the lab. Finally we incorporated the pipeline in describing several bacterial species from out lab. This thesis is subdivided mainly into Taxono-genomics and Microbiogenomics. The reviews in taxono-genomics section, describes about the technological advances in genomics and metagenomics relevant to the field of medical microbiology and describes the strategy taxono-genomics in detail and how polyphasic strategy along with genomic approaches are reformatting the definition of bacterial taxonomy. The articles describes clinically important bacteria, their whole genome sequencing and the genomic, comparative genomic and taxono-genomic studies of these bacteria.

8 Summary The thesis "The elucidation of the causes of neurogenetic diseases by the MPS data analysis using advanced algorithms" is focused on processing the massively parallel sequencing (MPS) data from a gene panel, whole-exome sequencing (WES) and whole-genome sequencing (WGS). The aim of the study was to develop a suitable pipeline to evaluate at least 250 MPS gene panel data, 150 WES data and 20 WGS data in order to improve molecular genetic testing of rare neurogenetic disorders. Associated data management and database implementation is also described. Targeted gene panel sequencing A custom-designed gene panel consisting of ge- nes previously associated with the disease was used. In the Epileptic Encephalopathy (EE) panel, two prerequisites need to be met for inclusion into the panel: the gene has to have been published in at least two independent publications OR at least in one publication but in multiple independent families. In the case of the EE panel, 112 genes were included. The targeted gene panel sequencing was then performed on 257 patients with EE. Pathogenic or likely pathogenic (according to ACMG criteria) variants have been found in 28% of patients (72 out of 257). Further analysis of the pathogenic or likely pathogenic variants was performed (76 in total); the variants were grouped by...

Determining the genetic cause of short stature as a way to understand the pathophysiological mechanisms affecting human growth Abstract Short stature is one of the most common disorders followed-up by a paediatric endocrinologist. Pathophysiologic mechanisms leading to growth disorders are complex, however, the exact cause is mostly unknown. Our study is the first to evaluate the aetiopathogenesis of familial short stature (FSS). Using next-generation sequencing (NGS) techniques, we aimed to describe the monogenic aetiology of growth impairment in a group of FSS families, and therefore to elucidate mechanisms leading to this specific growth disorder. In selected genetic diagnoses, we additionally aimed to describe the phenotype including GH treatment response. Within Motol University Hospital centre for GH therapy, we formed a group of 98 FSS families with clear height definition in ≤-2 SD in both the child height before GH therapy and in his shorter parent. Using NGS, the FSS aetiology was elucidated in 40/98 (41%) families; 32/40 had a genetic growth plate disorder. Within the cohort, three genetically homogeneous subgroups of families were described (collagenopathies - 10/98 [10.2%] families, SHOX deficiency - 6/98 [6.1%] families, and C type natriuretic peptide receptor disorder - 4/98 [4.1%] families)....

Deafblindness is a combined impairment of vision and hearing with an incidence of about 1: 8000 children and 1: 5500 adults. The most common genetic causes are the Stickler (STL) and Usher (USH) syndromes. The main goal of this work is to provide an up-to-date overview of STL and USH in the Czech and Slovak Republic (CR and SR), to determine the correlations between the genotype and phenotype in our population and the associated diagnostic criteria. Using sequencing and MLPA we examined 45 patients from 28 families for suspected STL. We found potentially causal variants of STL genes in 39 patients from 22 families. Fifteen different COL2A1 variants (8 being novel) were found in 28 patients from 18 families and 4 novel COL11A1 variants were found in 11 patients from 4 families. We identified the cause of the disease in 79 % of the families. The USH study involved 30 patients from 27 families. The most frequent cause was USH2A pathogenic variants, i.e. 19 variants in 14 families, 9 being novel. Less common were pathogenic variants in MYO7A (6 variants in 3 families, 5 being novel), USH1C and CDH23 (3 variants, 2 being novel, in 2 families both) genes. In 2 families, compound heterozygosity was found for variants in two different USH genes. The deafblindness etiology was clarified for 24 patients from...

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Theoretical part of this diploma thesis gives a brief characteristic of human mobile elements (transposons), which represents nearly 50% of human genome. It provides basic transposon clasification and describes types of transposons present in hunam genome, as well as mobilization, activation and regulation mechanisms. The work also deals with the domestication of transposons, describes the ways in which TE contribute to DNA damage and summarizes the diseases caused by mutagenic activity of transposons in the human genome. Conclusion of theoretical part describes next-generation sequencing technologies (NGS). As practical part, data from RNA-seq experimet were analyzed in order to compare differen transposon activity in normal and cancer cells from prostate and colorectal tissues. As like as publicly available sophisticated tools (TopHat), new scripts were created to analyze these data. The results show that cancer cells exhibit overexpression of transposons. This corresponds with the published results and suggests a connection of transposon activation with cancer development.

Les cancers du sein et de l’ovaire apparaissent dans 5 à 10% dans un contexte de prédisposition génétique, dont seule une faible part est expliquée par la présence d’un variant pathogène sur les gènes BRCA1, BRCA2 et PALB2. Le séquençage à haut-débit permet d’explorer cette hérédité manquante, mais représente un nouveau défi à la fois informatique, statistique et biologique. Trois approches utilisant cette nouvelle technologie ont été employées pour rechercher de nouveaux facteurs de prédisposition. En premier lieu, les risques associés à 34 gènes connus ou suspectés d’être impliqués dans les prédispositions ont été estimés à partir de l’analyse de 5 131 cas index et le développement d’une nouvelle approche statistique. Aussi la participation des néo-mutations en mosaïque dans le syndrome a été explorée à partir de 1 750 cas index issus de l’étude précédente, avec un logiciel de détection des variants faiblement représentés développé spécifiquement: outLyzer. Enfin, l’exploration par séquençage de l’hérédité manquante a été étendue à un panel de 201 gènes impliqués dans le cancer, à partir de 118 patientes sélectionnées pour la précocité d’apparition de leur maladie, élément fortement évocateur d’un facteur de prédisposition. Les résultats de ces travaux ont permis de valider la pertinence de l’étude de PALB2, RAD51C et RAD51D pour la prise en charge des patients, et suggèrent aussi une implication sous-estimée des variants en mosaïque. Cependant il reste encore très probablement d’autres facteurs génétiques fortement pénétrants à découvrir mais dont la modulation du risque répond à un modèle oligogénique. / Breast and ovarian cancers appear in 5 to 10% of cases in a context of genetic predisposition, of which only a small proportion is explained by the presence of a pathogenic variant on the BRCA1, BRCA2 and PALB2 genes. High throughput sequencing can explore this missing heredity, but represents a new challenge both in computing, statistics and biology. Three approaches using this new technology have been used to investigate new predisposition factors. First, the risks associated with 34 known or suspected genes involved in predispositions were estimated from the analysis of 5,131 index cases and the development of a new statistical approach. Also, the participation of mosaic neo-mutations in the syndrome was explored from 1,750 index cases from the previous study, with a software developed specifically for detecting poorly represented variants: outLyzer. Finally, the exploration by sequencing of the missing heredity was extended to a panel of 201 genes involved in cancer, from 118 patients selected for the early onset of their disease, a highly suggestive element of a predisposition factor. The results of this work validated the relevance of the PALB2, RAD51C and RAD51D study for patient management, and also suggested an underestimated involvement of mosaic variants. However, there are still very likely other highly penetrating genetic factors to be discovered, but whose risk modulation is based on an oligogenic model.

L’avènement du séquençage haut débit permet actuellement d’étudier et d’analyser la part de lacomposante génétique des maladies complexes médiée par les variants rares. Cependant, leurinterprétation représente un défi majeur. En effet, le séquençage de milliers d’exomes et degénomes a révélé la complexité du polymorphisme humain et notamment la surreprésentation devariants rares. Et malgré le développement de logiciels d’analyse ainsi que de différentes bases dedonnées, la priorisation des variants rares reste difficile. Dans le cadre de cette thèse, nous avons focalisé nos analyses sur les variations génétiques rares impliquées dans la maladie d’Alzheimer (MA). D’un point de vue génétique, la MA répond dans une majorité des cas à un déterminisme multifactoriel mais une minorité des cas sont des formes précoces à transmission autosomique dominante. La caractérisation des gènes PSEN1, PSEN2 et APP responsables des formes mendéliennes de MA a permis de formuler l’hypothèse de la cascade amyloïde en plaçant le peptide amyloïde (Aβ) au centre du processus physiopathologique. Afin de détecter de nouveaux facteurs de risque génétique dans la survenue de la MA, nous avons réalisé une étude d’association à partir de données de séquençage d’exomes de 522 cas atteints de formes précoces de MA et 584 contrôles. Les premières analyses ont porté sur les variants mononucléotidiques ainsi que les courtes insertions/délétions et ont permis de mettre en évidence un enrichissement en variants rares prédits délétères dans le gène ABCA7 chez les individus malades. Notre attention s’est ensuite portée sur les variations du nombre de copies (CNVs). L’absence de récurrence à l’échelle d’un gène nous a amené à travailler sur une liste de gènes. En nous focalisant sur l’hypothèse amyloïdergique, nous avons construit une liste de 342 gènes impliqués dans le métabolisme et la toxicité du peptide Aβ. Grâce à cette stratégie, nous avons ainsi réussi à mettre en évidence un enrichissement de CNVs rares intersectant ce réseau centré sur le peptide Aβ. Le résultat majeur de cette étude de CNVs a été la mise en évidence d’une duplication du locus 17q21.31 chez 5 patients atteints d’une maladie neurodégénérative similaire à une maladie d’Alzheimer. Les patients porteurs présentent un diagnostic clinique de MA, des biomarqueurs et une imagerie métabolique en faveur d’une neurodégénérescence de type Alzheimer. En revanche, l’imagerie amyloïde et l’analyse neuropathologique n’ont pas révélé de pathologie amyloïde et sont donc en faveur d’une tauopathie pure. L’étude des CNVs a également révélé une délétion partielle du gène PSEN1, emportant les exons 9 et 10, pour laquelle nous avons pu réaliser des études fonctionnelles. Nous avons ainsi pu déterminer que la protéine mutante favorisait la production de peptides amyloïdes plus longs, ces derniers étant des médiateurs majeurs de la neurotoxicité d’Aβ. / Next-generation sequencing allows studying and analyzing the genetic component part of complexdiseases mediated by rare variants. However, their interpretation represents a major challenge.Indeed, the sequencing of thousands of exomes and genomes revealed the human polymorphismcomplexity and in particular the overrepresentation of rare variants. Despite the development ofsoftwares and variant databases, the prioritization of rare variants remains arduous. My thesis subject was focused on the involvement of rare variants in Alzheimer's disease (AD). From a genetic point of view, AD is caused, in most cases, by a multifactorial determinism, but a minority of cases are autosomal dominant early-onset forms (ADEOAD). The characterization of mutations in the PSEN1, PSEN2 and APP genes as a cause of these Mendelian forms of AD led to the formulationof the amyloid cascade hypothesis, stating that the amyloid-β peptide (Aβ) is triggering the pathophysiological process. In order to detect new genetic risk factors involved in AD, we performed an association study using exome sequencing data from 522 cases with early-onset Alzheimer Disease and 584 controls. The first analyzes focused on single nucleotide variants and short insertions / deletions, and revealed an enrichment in cases of variants that are predicted to be deleterious in the ABCA7 genes. We then then focused on copy number variations (CNVs). The lack of recurrence at the gene-level incited us to work on a gene list. By focusing on the amyloidogenic hypothesis, we built a list of 342 genes involved in the metabolism and toxicity of the Aβ peptide. Thanks to this strategy, we found an enrichment of rare CNVs intersecting this Aβ network in cases.The main result of this CNV study was the identification of a duplication of the 17q21.31 locus in 5patients with a neurodegenerative disease similar to Alzheimer's disease. These patients have aclinical diagnosis of AD, as well as biomarkers and metabolic imaging consistent with an ADneurodegeneration. However, amyloid imaging and neuropathological analysis did not reveal anyamyloid pathology, and were therefore pointing to a pure tauopathy. This CNV study also revealed a partial deletion of the PSEN1 gene, overlapping exons 9 and 10, for which we performed functional studies. We demonstrated that the mutant protein enhanced the production of longer amyloid peptides, the latter being major mediators of Aβ neurotoxicity.

Le modèle ΛCDM permet de décrire avec une grande précision la plupart des présentes observations cosmologiques. Cependant, l'un de ses paramètres, σ 8, mesurant l'amplitude de fluctuations de la matière, présente une discordance entre sa valeur contrainte par le spectre de puissance angulaire du CMB de la mission Planck, les Cls, et celle déterminée à partir des amas SZ dans l'univers proche. Dans le présent travail on explore divers extensions du modèle ΛCDM comme origines possibles de cette anomalie. Pour tester les effets de ces extensions, nous avons effectué une analyse Monte Carlo on l'on compare les contraintes sur σ 8 à partir de ΛCDM avec celles résultantes de ces extensions, et ceci en utilisant principalement le spectre de puissance CMB seul ou combiné avec des comptages d'amas. Ces derniers sont basés sur différentes relations masse observables et couvrent différents redshift : des amas de rayons X dans l'univers local, des amas de la mission SZ Planck dans l'univers proche ou une estimation des amas détectés par leur richesse photométrique à partir du la future mission Euclid. Du fait qu'une mauvaise détermination de l'étalonnage de la masse des amas pourrait également être la raison de cette divergence, notre approche consistait, lorsqu'on combinait les deux sondes issues des amas et du CMB, à laisser le facteur d'étalonnage libre afin qu'il soit contraint comme les autres paramètres cosmologiques par les deux données. Dans le cas d'introduction de trois neutrinos massifs dégénérés, nous avons trouvé qu'ils n'ont aucun effet significatif sur la correction de l'écart entre les contraintes issues de comptage CMB et ceux issues des Xray ou SZ cluster. Nous avons ensuite permis à l'indice de croissance ƴ de varier. Nous trouvons une corrélation entre ƴ et le paramètre de calibration masse-observable des amas détectés par rayons X qui n'est pas affecté par la présence ou non des neutrinos massifs. [...] / The ΛCDM model has proved successful in describing to a high precision most of nowadays cosmological observations. However, one of its parameters, σ 8, measuring the present matter amplitude fluctuations, constrained from CMB angular power spectrum, the Cls, was found by the Planck mission, in significant tension with value constrained by SZ galaxy cluster counts in the near universe. In the present work we investigate extensions to ΛCDM model as possible origins behind this discrepancy. To test these extensions, we performed a Monte Carlo analysis to compare constraints on σ 8 in ΛCDM with constraints under these extensions, using mainly CMB Cls combined with cluster counts sample. The later were based on different mass observables relations and covered different redshift ranges: X-ray cluster in the local universe, SZ Planck mission clusters from the near universe or photometric richness estimated detected clusters from future high redshift upcoming Euclid alike mission. Because an improper determination of the calibration of cluster mass function could also be behind this discrepancy, our approach was, when combined with CMB, to leave the calibration factor free to vary and be constrained by data. Introducing three degenerate massive neutrinos, we found that they have no significant effect on fixing the discrepancy between CMB and Xray or SZ cluster counts. We then allowed the growth index ƴ to vary. We find a correlation in the confidence space between ƴ and the X-ray mass observable factor not affected by the presence of massive neutrinos, indicating that a modifying gravity is favored over massive neutrinos as a way to alleviate the tension. However, when a SZ cluster sample covering a larger redshift range was used, we found that the correlation between ƴ and the calibration factor, is constrained by the evolution of the growth through redshift and limited to a region where it cannot fix the discrepancy. [...]

MSc (Microbiology) / Department of Microbiology / Background: Antiretroviral treatment (ART) has grown to be one of the most effective tool in the fight to control HIV/AIDS morbidity and mortality worldwide. However, due to the emergence of drug resistant HIV, ART efficacy can be jeopardized. Drug resistant HIV strain has a potential of becoming a major public threat, as its limit treatment options on people living with HIV. With several findings worldwide reporting drug resistant HIV to be currently being transmitted to ART-naïve persons, measures have been taken to genotype drug resistant HIV prior to treatment initiation. However, in resource limited countries such measures are not executed especially in public sectors due to the costs associated with the required assays for genotyping. Objective: The objectives of the study was to establish a deep sequencing protocol (Next Generation Sequencing-NGS) using an Illumina MiniSeq Platform and subsequently apply it to genotype HIV in chronically infected drug naïve persons for resistance mutations and viral genotypes Methods: HIV positive Individuals without any exposure to ART (Treatment-naive) were recruited. Partial pol fragment (complete protease and ~1104bp reverse transcriptase) were amplified and purified. Libraries were prepared using Nextera XT library preparation kit, fragmented, tagmented, pooled and denatured then sequenced with Illumina MiniSeq instrument. Consensus sequences were derived, aligned and phylogenetically analysed. The Stanford HIV Drug Resistance Algorithm was used to infer the presence of drug resistant mutants, at the viral minority and majority population levels. Results and discussion: An NGS protocol to generate nucleotide sequences for drug resistance inference was established. No major drug resistance mutations were detected against protease, reverse transcriptase inhibitors in the study subjects investigated. Nevertheless, V179D change was observed in one patient (8.3%). V179D has been shown to impact a low-level resistance to NNRTI. On the other hand, several secondary and unusual mutations at known drug sites were detected even at minority threshold level of <20%. Conclusion: No major drug resistance mutations was detected in the drug naïve study population. This finding suggests that there is no risk of treatment failure to the investigated subjects, however it is important to assess the potential phenotypic v | P a g e significance of the identified secondary resistance mutations in the context of HIV-1 subtype C. The established NGS protocol should be applied in subsequent HIV drug resistance studies. / NRF