210 research outputs found
Optimization of genomic data analysis in rare diseases
No full textLes analyses pangénomiques d’exome et de génome ont permis d’augmenter considérablement le rendement diagnostique des maladies rares d’origine génétique au cours des dernières années, mais plus de 50 % des patients restent en impasse diagnostique (Wright, FitzPatrick, et Firth 2018). Pour les patients qui bénéficient d’un diagnostic, le délai d’obtention reste long, dépassant 5 ans pour 25 % des patients (Ministère des Solidarités et de la Santé 2019). L’absence de diagnostic ou le délai avant celui-ci sont une réelle perte de chance pour le patient et les familles, en termes de prise en charge de soin, mais également en termes de prise en charge sociale.L’objectif de la thèse est d’optimiser l’analyse de données génomiques dans les maladies rares, par l’implémentation de nouvelles approches, qu’elles soient organisationnelles, biologiques ou bioinformatiques, en vue d’obtenir un diagnostic plus rapidement dans un contexte d’urgence, et d’augmenter le rendement diagnostique. La thèse est divisée en trois axes d’optimisation.Le premier axe, l’optimisation organisationnelle, consiste en l’étude Fastgen, qui évalue la faisabilité de l’analyse accélérée de génomes short read en trio chez des enfants en réanimation ou soins intensifs, nécessitant un diagnostic génétique précoce pour orienter leur prise en charge. L’objectif était d’obtenir un résultat en moins de 45 jours. Un séquençage de génomes en trio a été réalisé chez 37 familles, conduisant à un diagnostic moléculaire chez 18/37 (49 %) enfants, avec une durée médiane de rendu de résultat de 42 jours.Le deuxième axe, l’optimisation biologique, consiste en l’étude de la cohorte unsolved cases du projet Solve-RD, qui vise à réduire l’impasse diagnostique par la réanalyse de données d’exomes de patients sans diagnostic et par la mise à disposition des données génomiques aux équipes du projet. Les données de 3576 exomes (1522 cas index et 2054 parents) ont été réanalysées selon une stratégie low-hanging fruit qui vise à rechercher les variations déjà rapportées dans ClinVar comme étant pathogènes ou probablement pathogènes. La réanalyse a permis d’identifier les variations causales chez 59 patients (3,9 %), dont 9 pour lesquels nous présentons les raisons de l’absence de diagnostic au moment de la première analyse et les leçons à en tirer.Le partage des données au sein de Solve-RD a facilité la construction d’une cohorte qui a permis d’établir la responsabilité du gène YWHAE dans un trouble du neurodéveloppement avec ou sans anomalies cérébrales, ce qui a mené à un diagnostic chez 7 sujets avec des variations perte de fonction de ce gène.Le troisième axe, l’optimisation bioinformatique, consiste en l’implémentation d’un pipeline utilisant les meilleurs outils de génotypage d’expansions de microsatellites à partir de données de génome short read, dans le but d’établir de nouveaux diagnostics. Nous avons évalué les 10 principaux outils de la littérature, en avons conservé 4 et les avons testés sur 23 locus impliqués en pathologie humaine sur notre cohorte de 323 génomes de sujets atteints de troubles du neurodéveloppement. Le pipeline développé a mené à l’identification d’une expansion de microsatellites pathologique pouvant prédisposer à une maladie neurodégénérative, considérée comme une donnée incidente car sans lien avec le phénotype du patient.Notre stratégie d’optimisation de l’analyse des données génomiques dans les maladies rares s’avère efficace : elle a permis de réduire l’errance diagnostique chez des enfants dans un contexte d’urgence et d’augmenter le rendement diagnostique du séquençage de l’exome et du génome short read par le développement de nouvelles stratégies d’analyse, de réanalyse et par le partage de données à large échelle.Exome and genome sequencing have significantly increased the diagnostic yield of rare genetic diseases in recent years, but more than 50% of patients remain in a diagnostic deadlock (1). For patients who are diagnosed, the time to obtain a diagnosis remains long, over 5 years for 25% of patients (2). The absence of diagnosis or the delay before it is made is a loss of chance for the patient and the families, in terms of care management, as well as in terms of social management.The objective of this work is to optimize the analysis of genomic data in rare diseases by implementing new approaches, whether they be organizational, biological or bioinformatics, to obtain a faster diagnosis in an emergency context and to increase the diagnostic yield. The thesis is divided into three optimization axes.The first axis deals with organizational optimization and consists of the Fastgen study, which assesses the feasibility of accelerated short read trio-genome analysis in children in intensive care unit requiring an early genetic diagnosis to guide their care management. The objective was to obtain a result in less than 45 days. Trio-genome analysis was performed in 37 families and led to a molecular diagnosis in 18/37 (49%) children, with a median time to result of 42 days.The second axis deals with biological optimization and consists of the study of the unsolved cases cohort of the Solve-RD project, which aims to reduce the diagnostic deadlock by reanalyzing exome data from patients without a diagnosis and by sharing genomic data with the project collaborators. Data from 3576 exomes (1522 index cases and 2054 relatives) were reanalyzed using a low-hanging fruit strategy that aims to search for variants already reported as pathogenic or probably pathogenic in ClinVar. The reanalysis identified causative variants in 59 patients (3.9%), including 9 for whom we present the reasons of the failure of the previous analyses and lessons learned.Data sharing within the Solve-RD consortium facilitated the construction of a cohort that established the involvement of the YWHAE gene in a neurodevelopmental disorder with or without brain abnormalities. This work led to a diagnosis in 7 subjects with loss-of-function variants in this gene.The third axis deals with bioinformatics optimization and consists in the implementation of a pipeline using the best tools to genotype microsatellite expansions from short read genome data, with the aim of establishing new diagnoses. We evaluated the 10 most popular tools in the literature and selected 4 of them. We tested them on 23 loci involved in human disease on our cohort of 323 genomes of subjects with neurodevelopmental disorders. This pipeline led to the identification of a pathological microsatellite expansion considered as an incidental finding because the variant was not related to the phenotype of the patient.Our strategy to optimize genomic data analysis in rare diseases is effective: it has reduced diagnostic odyssey, for children in urgent need for etiological diagnosis, and increased the diagnostic yield of exome and short read genome sequencing through the development of new strategies for analysis, re-analysis and large-scale data sharing
Epoxiconazole Exposure in C57Bl/6 Mice: Transgenerational Impacts on Hepatic Transcriptome and Methylome
No full textInternational audienceBackground:The pervasive use of phytosanitary products is invariably linked to concerns over environmental and health safety. Epoxiconazole (EPOX), a commonly employed fungicide, is of particular concern due to its potential transgenerational effects.Objectives:This study aimed to investigate the hepatic effects of epoxiconazole in the offspring of perinatally exposed low-dose C57Bl/6J mice, focusing on liver histological, transcriptomic, and epigenetic (DNA methylome) analyses.Methods:Only pregnant F0 C57BL6/J mice and their F1 offspring up to weaning were exposed to EPOX (1.75 µg/kg bw/day). F1 males and females were mated to generate the F2 generation, and similarly, F2 mice were crossed to obtain F3. Liver histological, transcriptome (micro-array), and methylome (Reduced representation bisulfite sequencing; RRBS) analyses were performed. Correlation analyses between transcriptomic and methylomic data were conducted for each generation and across generations to identify the underlying epigenetic mechanisms driving the observed alterations.Results and Conclusions:Perinatal exposure to EPOX induced complex transgenerational effects, manifesting as phenotypic, histological, transcriptomic, and epigenetic alterations in the liver. Methylome analyses revealed significant modifications in DNA methylation patterns, suggesting heritable epigenetic reprogramming. Correlation analyses highlighted strong associations between transcriptomic and methylomic changes, particularly in the regulatory regions of genes involved in hepatic metabolism, oxidative stress, and inflammatory processes. These findings suggest that EPOX induces enduring epigenetic alterations that contribute to the observed transgenerational effects, notably by altering gene expression in the liver
Author Correction: Postzygotic inactivating mutations of RHOA cause a mosaic neuroectodermal syndrome [Correction to: Nature Genetics https://doi.org/10.1038/s41588-019-0498-4, published online 30 September 2019]
No full textIndexation en cours. In the version of this article initially published, support from the Wellcome Trust and NIHR to author Veronica A. Kinsler was not included in the Acknowledgements. The error has been corrected in the HTML and PDF versions of the article.International audienceAn amendment to this paper has been published and can be accessed via a link at the top of the paper
Postzygotic BRAF p.Lys601Asn Mutation in Phacomatosis Pigmentokeratotica with Woolly Hair Nevus and Focal Cortical Dysplasia
No full textInternational audienc
Mutations in the ERCC2 (XPD) gene associated with severe fetal ichthyosis and dysmorphic features
No full textInternational audienceCongenital ichthyosis is a condition that includes several distinct subtypes with significant genetic heterogeneity. Defects in the ERCC2 [xeroderma pigmentosum (XP) complementation group D] gene lead to one of several clinical diseases, including XP, trichothiodystrophy, cerebrooculofacioskeletal syndrome, XP/Cockayne syndrome, and XP/trichothiodystrophy
FOXG1 variants can be associated with milder phenotypes than congenital Rett syndrome with unassisted walking and language development
No full textSince 2008, FOXG1 haploinsufficiency has been linked to a severe neurodevelopmental phenotype resembling Rett syndrome but with earlier onset. Most patients are unable to sit, walk, or speak. For years, FOXG1 sequencing was only prescribed in such severe cases, limiting insight into the full clinical spectrum associated with this gene. Next-generation sequencing (NGS) now enables unbiased diagnostics. Through the European Reference Network for Rare Malformation Syndromes, Intellectual and Other Neurodevelopmental Disorders, we gathered data from patients with heterozygous FOXG1 variants presenting a mild phenotype, defined as able to speak and walk independently. We also reviewed data from three previously reported patients meeting our criteria. We identified five new patients with pathogenic FOXG1 missense variants, primarily in the forkhead domain, showing varying nonspecific intellectual disability and developmental delay. These features are not typical of congenital Rett syndrome and were rarely associated with microcephaly and epilepsy. Our findings are consistent with a previous genotype-phenotype analysis by Mitter et al. suggesting the delineation of five different FOXG1 genotype groups. Milder phenotypes were associated with missense variants in the forkhead domain. This information may facilitate prognostic assessments in children carrying a FOXG1 variant and improve the interpretation of new variants identified with genomic sequencing
The oculoauriculofrontonasal syndrome: Further clinical characterization and additional evidence suggesting a nontraditional mode of inheritance
No full textThe oculoauriculofrontonasal syndrome (OAFNS) is a rare disorder characterized by the association of frontonasal dysplasia (widely spaced eyes, facial cleft, and nose abnormalities) and oculo-auriculo-vertebral spectrum (OAVS)-associated features, such as preauricular ear tags, ear dysplasia, mandibular asymmetry, epibulbar dermoids, eyelid coloboma, and costovertebral anomalies. The etiology is unknown so far. This work aimed to identify molecular bases for the OAFNS. Among a cohort of 130 patients with frontonasal dysplasia, accurate phenotyping identified 18 individuals with OAFNS. We describe their clinical spectrum, including the report of new features (micro/anophtalmia, cataract, thyroid agenesis, polymicrogyria, olfactory bulb hypoplasia, and mandibular cleft), and emphasize the high frequency of nasal polyps in OAFNS (56%). We report the negative results of ALX1, ALX3, and ALX4 genes sequencing and next-generation sequencing strategy performed on blood-derived DNA from respectively, four and four individuals. Exome sequencing was performed in four individuals, genome sequencing in one patient with negative exome sequencing result. Based on the data from this series and the literature, diverse hypotheses can be raised regarding the etiology of OAFNS: mosaic mutation, epigenetic anomaly, oligogenism, or nongenetic cause. In conclusion, this series represents further clinical delineation work of the rare OAFNS, and paves the way toward the identification of the causing mechanism
Correction: A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis (European Journal of Human Genetics, (2021), 29, 9, (1359-1368), 10.1038/s41431-021-00900-2)
No full textIn the original publication of the article, consortium author lists were missing in the article. The details are as below
Postzygotic KITLG mutation in a congenital non-progressive linear nevoid hyperpigmentation
No full textInternational audienc
Fifteen years of research on oral-facial-digital syndromes: from 1 to 16 causal genes
No full textInternational audienceOral-facial-digital syndromes (OFDS) gather rare genetic disorders characterised by facial, oral and digital abnormalities associated with a wide range of additional features (polycystic kidney disease, cerebral malformations and several others) to delineate a growing list of OFDS subtypes. The most frequent, OFD type I, is caused by a heterozygous mutation in the OFD1 gene encoding a centrosomal protein. The wide clinical heterogeneity of OFDS suggests the involvement of other ciliary genes. For 15 years, we have aimed to identify the molecular bases of OFDS. This effort has been greatly helped by the recent development of whole-exome sequencing (WES). Here, we present all our published and unpublished results for WES in 24 cases with OFDS. We identified causal variants in five new genes (C2CD3, TMEM107, INTU, KIAA0753 and IFT57) and related the clinical spectrum of four genes in other ciliopathies (C5orf42, TMEM138, TMEM231 and WDPCP) to OFDS. Mutations were also detected in two genes previously implicated in OFDS. Functional studies revealed the involvement of centriole elongation, transition zone and intraflagellar transport defects in OFDS, thus characterising three ciliary protein modules: the complex KIAA0753-FOPNL-OFD1, a regulator of centriole elongation; the Meckel-Gruber syndrome module, a major component of the transition zone; and the CPLANE complex necessary for IFT-A assembly. OFDS now appear to be a distinct subgroup of ciliopathies with wide heterogeneity, which makes the initial classification obsolete. A clinical classification restricted to the three frequent/well-delineated subtypes could be proposed, and for patients who do not fit one of these three main subtypes, a further classification could be based on the genotype
- …
