L'insuffisance surrénale primaire (ISP) se caractérise par un déficit en hormones stéroïdiennes lié à un trouble du cortex surrénal qui expose au risque d'insuffisance aiguë et de menace vitale. Actuellement, 80% des formes pédiatriques d'ISP sont d'origine génétique et 5% restent sans étiologie génétique identifiée. Les récentes découvertes de mutations de gènes du stress oxydant ouvrent le champ des recherches d'anomalies génétiques non spécifiques de la glande surrénale. Le séquençage parallèle massif (MPS) autorise aujourd'hui la réalisation de millions de séquences et l'étude simultanée de plusieurs gènes de plusieurs patients ce qui permet d'accélérer le diagnostic. C'est aussi la technique de choix pour la recherche de nouveaux gènes. Cependant, parmi les défis de cette nouvelle technologie, il est possible de citer la gestion de la très grande quantité de données qu'elle génère et le besoin d'une validation rigoureuse préalable à son utilisation à des fins diagnostiques.Le premier objectif du présent travail était d'établir un diagnostic génétique dans une cohorte de patients atteints d'ISP et de rechercher de nouveaux gènes. L'étude des génotypes et des phénotypes permet de comprendre les mécanismes physiopathologiques pour les engager dans le traitement et le conseil génétique.Le second objectif était le développement de méthodes bio-informatiques et d'inférence statistique pour faciliter le transfert du séquençage classique (Sanger) vers la technique MPS. Ce développement comprend l'analyse graphique de la qualité du séquençage, l'ajustement de modèles log-linéaires pour comparer les propriétés de différents « pipelines », et l'ajustement de modèles additifs généralisés pour estimer les contributions des sources d'erreurs de séquençage. Les analyses statistiques ont considéré chaque paire de bases comme unité statistique et chaque patient comme étude indépendante, ce qui confère à l'analyse simultanée de tous les patients le caractère d'une méta-analyse / Primary adrenal insufficiency (PAI) is characterized by an impaired production of steroid hormones due to an adrenal cortex defect. This condition exposes to the risk of acute insufficiency which may be life-threatening. Today, 80% of pediatric forms of PAI have a genetic origin but 5% have no clear genetic support. Recently discovered mutations in genes relative to the oxidative stress have opened the way to research works on genes unrelated to the adrenal gland. Massive Parallel Sequencing (MPS) is now able to perform millions of sequences and study simultaneously several genes in several patients, which accelerates the diagnosis. Above all, MPS is the preferred technique for new gene discoveries. However, among the challenges of this new technology one may cite the management of the huge amount of data MPS generates and the need for a strict validation process before the use of MPS for diagnosis purposes.The first objective of the present work was to establish a genetic diagnosis in a cohort of patients with PAI and search for new genes. Study the genotypes and phenotypes allows a better understanding of the physiopathological mechanisms of PAI and offering appropriate care for the patients and counseling for families. The second objective was the development of bioinformatic and statistical inference methods to help shifting from the classical Sanger sequencing to MPS. This shift involves a graphical analysis of the quality of sequencing, an adjustment of log-linear models to allow comparing the properties of different pipelines, an adjustment of the generalized additive models to allow estimating the contributions of various sources of sequencing errors. The statistical methods have considered each DNA base-pair as a statistical unit and each patient as a separate study which confers the simultaneous study of all patients the status of a meta-analysis

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Leukemia is the most common malignant disease in children patients. In our laboratory (CLIP) a novel subtype of B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL) with lineage switch during early phase of treatment towards myeloid lineage (swALL) was recently documented. SwALL incidence is almost 4 % of all BCP-ALLs (Slámová et al., 2014). DNA methylation (presence of 5-methylcytosine) is together with post-translational histone modifications and non- coding RNAs an epigenetic mechanism which regulates gene expression without changes of genetic code. DNA methylation is easily detected by bisulphite conversion and subsequent sequencing. The aim of this work was to compare genome-wide DNA methylation patterns between patients with swALL and control BCP-ALLs. The first step in achieving that was revision and improvement of bioinformatic processing protocol for eRRBS data from massive parallel sequencing. To improve the sequence adapter trimming I tested four bioinformatic tools - FAR, cutadapt, Trimmomatic and fastx_clipper. I implemented the fastest and most effective - Trimmomatic into the processing protocol. As a next step I analysed the data with improved protocol and extended the analysis in R programming environment where the comparison of studied groups was performed. The comparison of...

In comparison to men, the number of X-linked genes is doubled in women as they have two chromosomes X while men are hemizygotes for X-linked genes. This imbalance is compensated by X inactivation (XCI) process, also known as primary X-inactivation, occurring in the early stage of embryogenesis. X inactivation is a random process and females are mosaics of two cell populations. The ratio of expressed alleles in women can be random (50:50) or skewed (≥80:20). The skewed X inactivation may occur due to selection when one of the alleles is preferentially inactivated (secondary X inactivation). In this study XCI status in heterozygous females with various severity of phenotypic symptoms and traits in selected X linked inherited metabolic diseases is analysed, with the focus being Fabry disease - the deficiency of the enzyme alpha-galactosidase A encoded by GLA gene. Moreover, XCI in one family with X linked agammaglobulinemia is examined. Mutant alleles and XCI status based on various loci, different methodical approaches and different tissues is subjected to examination. For the first time, the direct analysis of GLA gene transcript to detect the allele ratio was used alongside with the single-nucleotide polymorphisms in the IDS and LAMP genes for allele-specific expression (ASE) and the AR, RP2 and...

<div><div>In the forensic science community, there is a vast need for tools to help assist investigations when standard DNA profiling methods are uninformative. Methods such as Forensic DNA Phenotyping (FDP) and proteomics aims to help this problem and provide aid in investigations when other methods have been exhausted. FDP is useful by providing physical appearance information, while proteomics allows for the examination of difficult samples, such as hair, to infer human identity and ancestry. To create a “biological eye witness” or develop informative probability of identity match statistics through proteomically inferred genetic profiles, it is necessary to constantly strive to improve these methods. </div><div><br></div><div>Currently, two developmentally validated FDP prediction assays, ‘HIrisPlex’ and ‘HIrisplex-S’, are used on the capillary electrophoresis to develop a phenotypic prediction for eye, hair, and skin color based on 41 variants. Although highly useful, these assays are limited in their ability when used on the CE due to a 25 variant per assay cap. To overcome these limitations and expand the capacities of FDP, we successfully designed and validated a massive parallel sequencing (MPS) assay for use on both the ThermoFisher Scientific Ion Torrent and Illumina MiSeq systems that incorporates all HIrisPlex-S variants into one sensitive assay. With the migration of this assay to an MPS platform, we were able to create a semi-automated pipeline to extract SNP-specific sequencing data that can then be easily uploaded to the freely accessible online phenotypic prediction tool (found at https://hirisplex.erasmusmc.nl) and a mixture deconvolution tool with built-in read count thresholds. Based on sequencing reads counts, this tool can be used to assist in the separation of difficult two-person mixture samples and outline the confidence in each genotype call.<br></div><div><br></div><div>In addition to FDP, proteomic methods, specifically in hair protein analysis, opens doors and possibilities for forensic investigations when standard DNA profiling methods come up short. Here, we analyzed 233 genetically variant peptides (GVPs) within hair-associated proteins and genes for 66 individuals. We assessed the proteomic methods ability to accurately infer and detect genotypes at each of the 233 SNPs and generated statistics for the probability of identity (PID). Of these markers, 32 passed all quality control and population genetics criteria and displayed an average PID of 3.58 x 10-4. A population genetics assessment was also conducted to identify any SNP that could be used to infer ancestry and/or identity. Providing this information is valuable for the future use of this set of markers for human identification in forensic science settings. </div></div><div><br></div>

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...

Massive parallel sequencing (MPS) data analysis tasks are often computationally demanding and their execution time would take too long using standard computing machines. Thus there is a need for parallelization of this tasks and ability to execute them on a sufficiently powerful computing machines. In the first chapter we describe a newly created platform for resequencing analysis of MPS data - MOLDIMED and novel annotation tool, which is ready to deploy on HPC infrastructure. The second chapter describes MPS approaches in Diamond-Blackfan anaemia (DBA), which is predominantly underlined by mutations in genes encoding ribosomal proteins (RP); however, its etiology remains unexplained in approximately 25% of patients. We performed panel sequencing of all ribosomal genes in DBA patient without previously known molecular pathology. A novel heterozygous RPS7 mutation coding RPS7 p.V134F was found in one female patient and subsequently confirmed in two asymptomatic family members, in whom mild anemia were detected on further examination. Subsequently, we performed whole transcriptome analysis in all family members and patient with RPS7 mutation in comparison with healthy control group and with DBA patients with known mutation in RPS19. We observed dysregulation mainly in signal pathways of translation,...

Examination of the genes DNM2, GARS, MORC2, TRPV4 and SOD1 among Czech patients with hereditary neuropathy axonal type For my PhD thesis I chose to work with patients with axonal form of CMT, because at that time axonal forms were less likely to be clarified by classical methods of molecular genetics. For further examination in patients with unclear cause of the axonal CMT, the genes DNM2, GARS and TRPV4 were selected. The aim was to determine the significance of pathogenic mutations in these genes as the cause of CMT2 in Czech patients. In the course, we identified causal variants in the genes MORC2 and SOD1 with WES. Therefore, we have tested additional CMT2 patients for the presence of these variants. Using Sanger sequencing, I examined a representative set of patients for the DNM2 (37), GARS (10) and TRPV4 (24) genes without finding a causal mutation, then we investigated genes SOD1 (43 patients) and MORC2 (161 patients). The cohort (50 patients) was also subjected to MLPA analysis using a P406-A1 CMT2 duplication and deletion detection kit for genes RAB7A, GARS, HSPB1, HSBP8 and SPTLC1 (kit P406-A1 CMT2). At that time, massively parallel sequencing (MPS) was becoming important. We compared the cost of classical sequencing versus MPS, and accordingly, we decided that the genes DNM2, GARS, MORC2, TRPV4...

Prenatal assessment of fetal health is routinely offered throughout pregnancy to ensure that the most effective management can be provided to maintain fetal and maternal well-being. Currently, invasive testing is used for definitive diagnosis of fetal aneuploidy, which is associated with a 1% risk of iatrogenic fetal loss. Developing non-invasive prenatal testing (NIPT) is a key area of research and methods to increase the level of cell-free fetal DNA (cffDNA) within the maternal circulation have been discussed to improve accuracy of such tests. In this study, three strategies; co-amplification at lower denaturation temperature polymerase chain reaction (COLD-PCR), inverse-PCR and Pippin Prep™ gel electrophoresis, were analysed to identify a novel approach to selectively enrich shorter cffDNA fragments from larger maternal cell-free DNA (cfDNA). The sensitivity of droplet digital PCR (ddPCR) against real-time PCR (qPCR) was compared for fetal sex and RHD genotyping. In addition RHD zygosity testing was carried out for non-maternal samples. Consequently, Pippin Prep™ gel electrophoresis was combined with ddPCR analysis for the NIPD of Down Syndrome (DS) in pseudo-maternal samples. The results revealed that the Pippin Prep™ gel electrophoresis enrichment approach successfully demonstrated 2-fold to 5-fold increases in the cffDNA fraction. However, further optimisation assays of COLD-PCR and inverse-PCR using actual maternal samples were required. The spike experiments for DS detection revealed that with the present assay IV overrepresentation of the chromosome 21 target could be significantly detected for samples with ≥15% ‘cffDNA fraction’. In conjunction with the Pippin Prep™ enrichment method, this would have enabled assessment of all 10 maternal samples. Alternatively, fetal sex and RHD genotyping results determined that ddPCR provides a more sensitive platform compared to qPCR approaches, particularly for samples that express low cffDNA fractions (<2%). The ddPCR platform also proved to be a rapid and accurate system for the determination of RHD zygosity. This study highlights that ddPCR could be used as opposed to qPCR for accurate determination of fetal sex and RHD status. While sequencing approaches currently provide the most sensitive platforms for NIPT of fetal aneuploidy, high costs (>£400) prevent universal application. The combination of cffDNA enrichment with ddPCR analysis could provide a cheaper and more widely available platform for NIPD. However, further large scale validation studies using actual maternal samples are required.