Letteratura scientifica selezionata sul tema "Séquençage à haut débit (NGS)"
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Articoli di riviste sul tema "Séquençage à haut débit (NGS)"
Hureaux, Marguerite, Laurence Heidet, Rosa Vargas-Poussou e Guillaume Dorval. "Les grandes avancées en néphro-génétique pédiatrique". médecine/sciences 39, n. 3 (marzo 2023): 234–45. http://dx.doi.org/10.1051/medsci/2023028.
Testo completoCoquerelle, S., M. Darlington, N. Mezaour, C. Preudhomme, E. Mc Intyre e I. Durand-Zaleski. "Séquençage Haut Débit (NGS) dans les hémopathies malignes et évaluation médico-économique–PRME RUBIH2". Revue d'Épidémiologie et de Santé Publique 67 (giugno 2019): S190. http://dx.doi.org/10.1016/j.respe.2019.04.049.
Testo completoLe Cann, Pierre, Delphine Méheust, Tina Reponen, Stephen Vesper e Jean-Pierre Gangneux. "Intérêt du séquençage haut-débit (NGS) sur prélèvements d’air pour la caractérisation de l’exposition fongique domiciliaire". Journal de Mycologie Médicale 25, n. 3 (settembre 2015): 222. http://dx.doi.org/10.1016/j.mycmed.2015.06.013.
Testo completoUch, R., R. Barre, F. Jordier, P. De Micco e P. Biagini. "Apport du séquençage à haut débit NGS dans la détection de séquences virales : application à des dons de sang à marqueurs viraux positifs". Transfusion Clinique et Biologique 22, n. 4 (settembre 2015): 227. http://dx.doi.org/10.1016/j.tracli.2015.06.041.
Testo completoTaudière, Adrien. "Déterminants de la structure des communautés fongiques dans les forêts de Corse : rôle des perturbations et de la composition forestière". BOIS & FORETS DES TROPIQUES 334 (2 gennaio 2018): 75. http://dx.doi.org/10.19182/bft2017.334.a31493.
Testo completoAudebert, Christophe, David Hot, Yves Lemoine e Ségolène Caboche. "Le séquençage haut-débit". médecine/sciences 30, n. 12 (dicembre 2014): 1144–51. http://dx.doi.org/10.1051/medsci/20143012018.
Testo completoRodriguez, Christophe. "Aspects techniques du séquençage à haut débit". Revue Francophone des Laboratoires 2022, n. 541 (aprile 2022): 55–59. http://dx.doi.org/10.1016/s1773-035x(22)00136-8.
Testo completoRodriguez, Christophe. "Aspects techniques du séquençage à haut débit". Revue Francophone des Laboratoires 2022, n. 541 (aprile 2022): 55–59. http://dx.doi.org/10.1016/s1773-035x(22)00136-8.
Testo completoFoulongne, V., V. Sauvage, C. Hebert, O. Dereure e M. Eloit. "Virome cutané : étude systématique par séquençage haut débit". Annales de Dermatologie et de Vénéréologie 140, n. 12 (dicembre 2013): S581—S582. http://dx.doi.org/10.1016/j.annder.2013.09.496.
Testo completoAudebert, Christophe, David Hot e Ségolène Caboche. "Séquençage par nanopores". médecine/sciences 34, n. 4 (aprile 2018): 319–25. http://dx.doi.org/10.1051/medsci/20183404012.
Testo completoTesi sul tema "Séquençage à haut débit (NGS)"
Becmeur-Lefebvre, Mathilde. "Identification de nouveaux genes responsables d'anomalies du développement par séquençage haut débit d'exome". Thesis, Bourgogne Franche-Comté, 2019. http://www.theses.fr/2019UBFCK080.
Testo completoMultiple congenital anomalies (MCA) are often genetic conditions, with a risk of recurrence. The etiologic diagnosis of these conditions in fetuses is mandatory to allow genetic counseling for the future pregnancies. Regarding current diagnostic tests (fetal autopsy, cytogenetic test and targeted molecular tets), the diagnostic rate in MCA fetuses is about 30%, allowing genetic counselling in only one third of families. Exome sequencing (ES) has allowed to identify the molecular basis of many new syndromes.We aimed to assess the contribution of ES solo-based strategy to identify new developmental genes in fetuses presenting with MCA without etiological diagnosis after standard investigations with an original multistep strategy.We performed solo ES in 95 MCA fetuses from 10 prenatal diagnostic centers in France. First, we focused on OMIM related disease genes, with a first step using bioinformatic scores and public databases independently of phenotype, a second step using genotype-phenotype correlation and a third step of research analysis extended to the whole exome. Variant confirmation and parental segregation were done by Sanger sequencing. ES allowed the identification of a causative variants in 23 fetuses (24%), variants of unknown significance (VUS) in 7 fetuses (7%) and variants in new candidate genes in 6 fetuses (6%). Among causative variants, most were from autosomal recessive inheritance (50%), 42% were sporadic and 4% were from autosomal dominant inheritance. The additionnal strategy identified 17/23 causative variants, including 2 new causative variants not identified by the classical approach because of atypical or extreme fetal phenotype, and 2 new VUS. No new candidate gene was identified by this strategy.To conclude, solo ES with classical and additionnal strategy presents a low efficiency to identify new genes implicated in embryonary development but allows the extension of the clinical spectrum of well-known pediatric pathologies to the prenatal period. Trio ES or genome sequencing would be now insteresting strategies to be explored
Lacoste, Deixonne Caroline. "Apport du séquençage haut débit dans l'amélioration de la prise en charge des maladies monogéniques". Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM5062/document.
Testo completoThe diffusion of Next Generation Sequencing (NGS) technologies induces an important change that modifies molecular diagnostics indications and prompts laboratories to re-think their diagnostic strategies, up-to-now based on Sanger sequencing routine. Several high throughput approaches are available from the sequencing of a gene panel, to a whole exome, or even a whole genome. In all cases, a tremendous amount of data are generated, that have to be filtered, interpreted and analyzed by the use of powerful bioinformatics tools.In part 1, existing strategies and the difficulties and challenges of high-throughput sequencing for molecular diagnosis in genetic diseases are discussed. In part 2, the set up and the technical validation of this diagnostic approach in the Molecular Genetics’ Laboratory of the Timone Hospital in Marseille is presented and illustrated by 3 examples of complex diagnostics solved thanks to NGS. NGS promises to shorten significantly the time of analysis and results reporting, and to expand the number of tested genes. It also promises to increase the proportion of positive diagnoses. Finally, the NGS can identify new variants and new genes involved in human pathology, thus will globally improve patient clinical care
Bisseux, Maxime. "Dynamique de la circulation des Entérovirus de l'homme à l'environnement : Etude par séquençage haut débit". Thesis, Université Clermont Auvergne (2017-2020), 2017. http://www.theses.fr/2017CLFAS013.
Testo completoEnterovirus (EV) are Picornaviruses (non-enveloped, positive-sense RNA viruses), characterized by a large genetic and antigenic diversity (116 types classified within 4 taxonomic species EV-A to D) and rapid evolution. Human infections are frequent, highly contagious from stools and occur as outbreaks. The infections are mainly asymptomatic or benign but severe or fatal cases can be reported in young children. Poliomyelitis is the model EV infection. Combined with clinical and virological surveillance, mass vaccination is closer than ever to achieve the WHO program of the Global Polio Eradication Initiative. However, the detection of wild type polioviruses in polio-free countries and the recent worldwide emergence of non-polio enteroviruses (EV-A71, EV-D68) associated with severe clinical manifestations underscore the importance of surveilling EV circulation in the general population. The aim of the PhD thesis was the detection and identification of EV strains in wastewater treated in the sewage treatment plant at Clermont-Ferrand (France). The viral data were compared with those reported through clinical surveillance to obtain a comprehensive picture of the viral circulation in the local population. A method was developed to concentrate viruses from raw and treated wastewater and molecular assays were used to detect EVs and 6 other human enteric viruses. The viral genomes were detected in all samples from October 2014 to October 2015, with a median of 6 and 4 different viruses in raw and treated wastewater respectively. Phylogenetic analysis of viral sequences (EV, hepatitis A and E viruses) determined in wastewater and reported in patients during the sampling period, showed the efficiency of the method for surveilling enteric viruses in the community. The EV diversity in raw wastewater was analyzed by sequencing of amplicons with the Illumina high throughput technology (metabarcoding). The analysis revealed a large viral diversity and the silent circulation of 25 types not detected from hospital data (in particular 9 EV-C, of which sequences of vaccine poliovirus 1). The phylogenetic analyses of intra-typic variants showed different epidemic patterns in the predominant EV types circulating over the study period. The data demonstrate the feasibility and sensitivity of the strategy developed for the detection and characterization of EV in wastewater and provide a future prospect for the implementation of environmental surveillance of non-polio EV infections in epidemiological studies, epidemic prevention, and for health alert. Combining the surveillance of enteric viruses in the environment and in the clinical setting allows a better understanding of their prevalence. This global approach of virus circulation and ecological health represents an important investment for laboratories, which will require integration in national and international collaboration networks beyond the scope of enterovirus surveillance
Croville, Guillaume. "Séquençage et PCR à haut débit : application à la détection et la caractérisation d'agents pathogènes respiratoires aviaires et au contrôle de pureté microbiologique des vaccins". Thesis, Paris Sciences et Lettres (ComUE), 2017. http://www.theses.fr/2017PSLEP028/document.
Testo completoDetection of pathogens becomes an increasing challenge, since infectious diseases represent major risks for both human and animal health. Globalization of trade and travels, evolution of farming practices and global climatic changes, as well as mass migrations are impacting the biology of pathogens and their emerging potential. This manuscript describes three approaches, based on three innovative technologies of molecular biology applied to the detection of pathogens in three different settings : (i) detection of a list of pathogens using real-time quantitative PCR on a microfluidic platform, (ii) unbiased detection of pathogens in complex matrix, using metagenomics and Illumina (Miseq) sequencing and (iii) genotyping of pathogens without isolation of PCR-enrichment using a 3rd generation NGS (Next Generation Sequencing) platform MinION from Oxford Nanopore Technologies. The three studies shown the contribution of these techniques, each representing distinctive features, suitable for the respective applications. Beyond application of these techniques to the field of microbial diagnostics, their use for the control of veterinary immunological drugs is a priority of this project. Veterinary vaccines are not only submitted to mandatory detection of listed pathogens to be excluded, but also to validation of the genetic identity of vaccine strains. The exponential availability and performances of new PCR or sequencing technologies open cutting-edge perspectives in the field of microbial diagnostic and control
Mansour-Hendili, Lamisse. "Mise en place d’une stratégie de validation fonctionnelle de variations de signification incertaine dans les pathologies constitutionnelles du globule rouge". Electronic Thesis or Diss., Paris 12, 2022. http://www.theses.fr/2022PA120057.
Testo completoThe deployment of next generation sequencing (NGS) over the past ten years in hospital genetic laboratories in France and around the world has revolutionized the management of rare diseases, including constitutional hemolytic anemia (CHA). It has led to the multiplication of variations of uncertain significance (VUS) requiring the implementation of functional tests to permit a re-classification. The objective of this work is to propose a realistic and effective strategy for the functional exploration of VUS associated with CHs. This approach is based on family genetic studies, study of transcripts on Paxgene tubes, development of methods on-site such as the LORRCA MaxSis for the study of the RBC membrane properties, improvment of techniques such as the RBC density measurement by phthalate gradient and establishment of a collaborative network (example of CNRS in Roscoff for electrophysiological studies). We have shown the interest of NGS in these patients with suspected CHA and have highlighted associations of variations of interest in different genes of RBC pathologies in the same patient (Mansour-Hendili et al 2020). We identified a new pathological entity in two patients with “autoimmune direct antiglobulin test negative” haemolytic anemia who did not respond to immunomodulators. This is a mechanism of acquired spherocytosis by point mutation of the ANK1 gene probably due to clonal hematopoiesis in the elderly (submission in progress). The realization of a whole genome sequencing led to a diagnosis for a child suffering from unexplained transfusion-dependent hemolysis with neurodevelopmental delay due to the VPS4A gene (Lunati-Rozie et al 2021). Via a patient recall system, additional explorations have been carried out. Twenty-five patients underwent a transcript study allowing the reclassification of sixteen variations. Ten family studies have been carried out, one of which excludes the deleterious nature of a VUS of the GATA1 gene. We have shown the interest of measuring RBC density as screening tool for RBC membrane diseases. Its use as a functional test in the case of associations of variations in RBC membrane genes has highlighted the usefulness of the dense cell rate as a differential marker of the presence/absence of the associated variation. Concerning the LORRCA, osmoscan profiles make it possible to discriminate patient with associations of variations compared to “positive” controls without association. Stability studies conducted for these phenotypic tests at different storage times and temperatures show the importance of pre-analytical conditions. We illustrated this problem with the known KCNN4 gene mutation: p.R352H described with a normal osmoscan and ektacytometry profiles. We found twice on two independent samples and manipulations realized on D0 without storage abnormal osmoscan profiles. In addition, we show the interest of the study of electrophysiological properties of the PIEZO1 and KCNN4 channels carried out in Roscoff in the classification of VUS (case one patient with a new KCNN4 mutation and thrombosis, Mansour-Hendili et al 2021). For the associations of variations of interest, the interpretation profiles are more complex but also show profiles differences compared to well-chosen controls. This work has made it possible to demonstrate the usefulness, in addition to family and transcript studies, of RBC phenotypic diagnostic or monitoring tools (LORRCA, density of the GR) to help with the functional validation of isolated or associated VUS in CHA patients. This requires means of revocation, adequate positive controls (intrafamilial cases) and compliance with preanalytical conditions. The establishment of collaborative networks also brings real usefulness and reciprocal intellectual and human added value. The return to the phenotype is an essential recourse for the classification of VUS in particular for the CHA
Piorkowski, Geraldine. "Étude des quasi-espèces du virus Ebola en réponse au traitement par favipiravir dans un modèle de primate non-humain par séquençage haut débit". Thesis, Aix-Marseille, 2019. http://www.theses.fr/2019AIXM0216.
Testo completoEbola virus disease (EVD) is a major public health issue due to the lack of antiviral treatment or candidate vaccine receiving market authorisation. The scope of the recent outbreaks (2014-2016 and 2018) has highlighted the urgent need to develop efficient treatments.The first scope of this thesis concerns the implementation of a non-human model (Mauritian Cynomolgus Macaques) of Ebola virus (EBOV-Gabon 2001 strain) infection. Following intramuscular administration of EBOV, vital parameters and viral genomic evolution (consensus mutations and viral quasi species) over the disease course were observed. Results demonstrated that evolution of EVD, in this model, is closer from human than previously described models (clinical, biological parameters deteriorate later, and death occurs later). Lethality is 100%. Viral variability is low and infectious dose has a limited impact on disease course.The second scope would highlight the antiviral efficacy of different favipiravir (T-705) doses (100, 150, 180mg/kg) administrated intravenously in this model. Clinical, biological parameters and viral variability were evaluated during disease course. The highest favipiravir dose administration (180 mg/kg) was associated with 60% of monkeys’ survival.Next generation sequencing of viral quasi species over disease course has given some insights into the Proposed mechanism of action of favipiravir. Viral quasi specie number was increased by five between treated monkeys and negative controls. Favipiravir is a GTP analogue inhibiting viral polymerase which induces C to T and G to A mutations leading to error catastrophe mechanism
Robitaille, Alexis. "Detection and identification of papillomavirus sequences in NGS data of human DNA samples : a bioinformatic approach". Thesis, Lyon, 2019. http://www.theses.fr/2019LYSE1358.
Testo completoHuman Papillomaviruses (HPV) are a family of small double-stranded DNA viruses that have a tropism for the mucosal and cutaneous epithelia. More than 200 types of HPV have been discovered so far and are classified into several genera based on their DNA sequence. Due to the role of some HPV types in human disease, ranging from benign anogenital warts to cancer, methods to detect and characterize HPV population in DNA sample have been developed. These detection methods are needed to clarify the implications of HPV at the various stages of the disease. The detection of HPV from targeted wet-lab approaches has traditionally used PCR- based methods coupled with cloning and Sanger sequencing. With the introduction of next generation sequencing (NGS) these approaches can be improved by integrating the sequencing power of NGS. While computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate bioinformatic tool has been available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. In this thesis, we initially describe five fully reconstructed novel HPV genomes detected from skin samples after amplification using degenerate L1 primers. Then, is the second part, we present PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify known and potentially new Papillomaviridae sequences from NGS amplicon sequencing with degenerate PV primers. This thesis describes the features of PVAmpliconFinder and presents several applications using biological data obtained from amplicon sequencing of human specimens, leading to the identification of new HPV types
Jourdain, Anne-Sophie. "Déterminisme moléculaire du développement des membres : apport des nouvelles technologies d’étude du génome". Thesis, Lille 2, 2019. http://www.theses.fr/2019LIL2S037.
Testo completoLimbs development is a complex process of which mecanism is today only partially known. Embryological development abnormalities of genetic origins are rare entities. Such abnormalities can be unique or multiple, single or syndromic, sporadic or of family origins.The study of large cohorts of patients carrier of limb extremities malformations is an excellent tool that allows an identification of the genes or regulatory elements involved in their pathology and consenquently, in the development of the limb. In most of the cases, the genetic event involved is a point mutation in the genes coding transcriptionnal factor or regulatory sequence. However, variations in the number of copies are also involved.Today, new technologies of genome study, from high through put sequencing of a target genes panel to a whole exome or genome sequencing, can allow an identification of these new targets. It is thank to these technological advances that we decided to study the moleculary determinism of limbs development. To do so, we analyzed a very large cohort of 684 patients, all carriers of a limb malformation, through different genes panels, of different sizes, but also through a whole exome analysis and a pangenomic CGH array.The results of this work allowed us, in the first part, to establish a genes panel, suitable to a molecular analysis laboratory, to the bioinformatic analysis with an optimized cost, and that can identify the SNVs but also the CNVs in only one analysis.On a second part, we managed to identify 5 genes, not yet described in human pathology, which seemed to have a role in limb development. For one of these genes a promising functional analysis has started
Rudewicz, Justine. "Méthodes bioinformatiques pour l'analyse de données de séquençage dans le contexte du cancer". Thesis, Bordeaux, 2017. http://www.theses.fr/2017BORD0635/document.
Testo completoCancer results from the excessive proliferation of cells decending from the same founder cell and following a Darwinian process of diversification and selection. This process is defined by the accumulation of genetic and epigenetic alterations whose characterization is a key element for establishing a therapy that would specifically target tumor cells. The advent of new high-throughput sequencing technologies enables this characterization at the molecular level. This technological revolution has led to the development of numerous bioinformatics methods. In this thesis, we are particularly interested in the development of new computational methods for the analysis of sequencing data of tumor samples allowing precise identification of tumor-specific alterations and an accurate description of tumor subpopulations. In the first chapter, we explore methods for identifying single nucleotide alterations in targeted sequencing data and apply them to a cohort of breast cancer patients. We introduce two new methods of analysis, each tailored to a particular sequencing technology, namely Roche 454 and Pacific Biosciences. In the first case, we adapted existing approaches to the particular case of transcript sequencing. In the second case, when using conventional approaches, we were confronted with a high background noise resulting in a high rate of false positives. We have developed a new method, MICADo, based on the De Bruijn graphs and making possible an effective distinction between patient-specific alterations and alterations common to the cohort, which makes the results usable in a clinical context. Second chapter deals with the identification of copy number alterations. We describe the approach put in place for their efficient identification from very low coverage data. The main contribution of this work is the development of a strategy for statistical analysis in order to emphasise local and global changes in the genome that occurred during the treatment administered to patients with breast cancer. Our method is based on the construction of a linear model to establish scores of differences between samples before and after treatment. In the third chapter, we focus on the problem of clonal reconstruction. This problem has recently gathered a lot of interest, but it still lacks a well-established formal framework. We first propose a formalization of the clonal reconstruction problem. Then we use this formalism to put in place a method based on Gaussian mixture models. Our method uses single nucleotide and copy number alterations - such as those discussed in the previous two chapters - to characterize and quantify different clonal populations present in a tumor sample
Nemoz, Benjamin. "Exploration longitudinale à haut débit et en cellule unique du répertoire d'anticorps neutralisants à large spectre chez un neutraliseur d'élite du VIH-1". Electronic Thesis or Diss., Université Grenoble Alpes, 2024. http://www.theses.fr/2024GRALV012.
Testo completoHuman Immunodeficiency Virus type 1 (HIV-1) infection remains a major global health concern, with an estimated 37.7 million people living with the virus worldwide and new contaminations above a million cases yearly. Efficient anti-retroviral therapies are available, allowing a sustained relief for infected individuals. These therapeutics have also contributed to a better prevention and helped curb the epidemic, notably in high-income countries. However, a vaccine is still highly awaited for controlling this epidemic, especially in lower-income regions and precarious settings.The protective role of neutralizing antibodies (NAbs) has been unequivocally demonstrated in both animal models of HIV infection and in human settings. Consequently, the development of a B-cell-based vaccine capable of eliciting antibodies (Abs) with the ability to neutralize the majority of circulating viruses, namely broadly NAbs (bNAbs), could be foreseen as an answer to the HIV pandemic.The investigation of bNAb development in HIV-1 elite neutralizers provides valuable insights to inform the design of such vaccines. To date, most of the undertaken studies have relied on conventional single B-cell FACS sorting to isolate bNAbs. In the present study, we have used the Chromium Single Cell Immune Profiling approach to conduct a high-throughput longitudinal single-cell exploration of the B-cell repertoire in an HIV-1 elite neutralizer. Importantly, this novel method enables the use of a much greater number of HIV envelope glycoprotein (Env) baits compared to regular FACS-based Ab isolation studies, providing a more comprehensive view of the anti-Env Ab repertoire. In addition, this approach yields a wealth of information on the nature of the specific Abs identified and the corresponding B-cells.The study enabled the uncovering of the sequence of 12,130 putative HIV Env specific Abs. Antibodies from 39 lineages were produced and tested for neutralization, revealing 21 distinct neutralizing lineages. The results thus demonstrated the ability of the method to explore large antigen-specific Ab repertoires from longitudinal samples. The neutralizing activity of Abs from four neutralizing lineages together recapitulated the serum activity of the donor, achieving neutralization against 62.4 % of a large predictive panel of 126 pseudoviruses. One of these neutralizing Ab lineages was shown to target the gp120 high-mannose patch supersite with great breadth and potency; Abs from this lineage were sensitive to the presence of a glycan in position N332. A single of those Abs achieved most of the neutralization breadth (51.1 %) with a high potency (mean IC50 of 91.1 ng.mL-1). This Ab exhibited a 23 AA-long CDRH3 and 20 % somatic hypermutation (SMH). The lineage showed continuous evolution over 6.5 years of maturation, with observed SHM rates ranging from 2.0 % to 30.6 % for the heavy chain, without any insertions or deletions.Conventional FACS-based sorting was previously used to isolate bNAbs from the same donor. In comparison, the single cell high-throughput approach made possible the isolation of orders of magnitude more Abs. Furthermore, the newly isolated NAbs were overall more potent and broader than those isolated previously, indicating the superiority of the novel method in recovering neutralizing lineages. Ongoing structural studies will elucidate the epitopes responsible for the broad neutralization observed in this donor. Together, the findings may help the design of reverse vaccine approaches, which show promise in the development of an effective AIDS vaccine
Capitoli di libri sul tema "Séquençage à haut débit (NGS)"
PIERELLA KARLUSICH, Juan José, Charlotte NEF, Chris BOWLER e Richard G. DORRELL. "Modèles biogéographiques et génomes des photoautotrophes aquatiques". In Planète bleue, photosynthèse rouge et verte, 45–82. ISTE Group, 2023. http://dx.doi.org/10.51926/iste.9082.ch3.
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