Complex nature of apparently balanced chromosomal rearrangements in patients with autism spectrum disorder

Background: Apparently balanced chromosomal rearrangements can be associated with an abnormal phenotype, including intellectual disability and autism spectrum disorder (ASD). Genome-wide microarrays reveal cryptic genomic imbalances, related or not to the breakpoints, in 25% to 50% of patients with an abnormal phenotype carrying a microscopically balanced chromosomal rearrangement. Here we performed microarray analysis of 18 patients with ASD carrying balanced chromosomal abnormalities to identify submicroscopic imbalances implicated in abnormal neurodevelopment. Methods: Eighteen patients with ASD carrying apparently balanced chromosomal abnormalities were screened using single nucleotide polymorphism (SNP) arrays. Nine rearrangements were de novo, seven inherited, and two of unknown inheritance. Genomic imbalances were confirmed by fluorescence in situ hybridization and quantitative PCR. Results: We detected clinically significant de novo copy number variants in four patients (22%), including three with de novo rearrangements and one with an inherited abnormality. The sizes ranged from 3.3 to 4.9 Mb; three were related to the breakpoint regions and one occurred elsewhere. We report a patient with a duplication of the Wolf-Hirschhorn syndrome critical region, contributing to the delineation of this rare genomic disorder. The patient has a chromosome 4p inverted duplication deletion, with a 0.5 Mb deletion of terminal 4p and a 4.2 Mb duplication of 4p16.2p16.3. The other cases included an apparently balanced de novo translocation t(5;18)(q12;p11.2) with a 4.2 Mb deletion at the 18p breakpoint, a subject with de novo pericentric inversion inv(11)(p14q23.2) in whom the array revealed a de novo 4.9 Mb deletion in 7q21.3q22.1, and a patient with a maternal inv(2)(q14.2q37.3) with a de novo 3.3 Mb terminal 2q deletion and a 4.2 Mb duplication at the proximal breakpoint. In addition, we identified a rare de novo deletion of unknown significance on a chromosome unrelated to the initial rearrangement, disrupting a single gene, RFX3. Conclusions: These findings underscore the utility of SNP arrays for investigating apparently balanced chromosomal abnormalities in subjects with ASD or related neurodevelopmental disorders in both clinical and research settings

Haploinsufficiency for ANKRD11-flanking genes makes the difference between KBG and 16q24.3 microdeletion syndromes:12 new cases

16q24 deletion involving the ANKRD11 gene, ranging from 137 kb to 2 Mb, have been associated with a microdeletion syndrome characterized by variable cognitive impairment, autism spectrum disorder, facial dysmorphisms with dental anomalies, brain abnormalities essentially affecting the corpus callosum and short stature. On the other hand, patients carrying either deletions encompassing solely ANKRD11 or its loss-of-function variants were reported in association with the KBG syndrome, characterized by a very similar phenotype, including mild-to-moderate intellectual disability, short stature and macrodontia of upper incisors, with inter and intrafamilial variability. To assess whether the haploinsufficiency of ANKRD11-flanking genes, such as ZFPM1, CDH15 and ZNF778, contributed to either the severity of the neurological impairment or was associated with other clinical features, we collected 12 new cases with a 16q24.2q24.3 deletion (de novo in 11 cases), ranging from 343 kb to 2.3 Mb. In 11 of them, the deletion involved the ANKRD11 gene, whereas in 1 case only flanking genes upstream to it were deleted. By comparing the clinical and genetic features of our patients with those previously reported, we show that the severity of the neurological phenotype and the frequency of congenital heart defects characterize the deletions that, besides ANKRD11, contain ZFPM1, CDH15 and ZNF778 as well. Moreover, the presence of thrombocytopenia and astigmatism should be taken into account to distinguish between 16q24 microdeletion syndrome and KBG syndrome. The single patient not deleted for ANKRD11, whose phenotype is characterized by milder psychomotor delay, cardiac congenital malformation, thrombocytopenia and astigmatism, confirms all this dat

Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features

SOX5 encodes a transcription factor involved in the regulation of chondrogenesis and the development of the nervous system. Despite its important developmental roles, SOX5 disruption has yet to be associated with human disease. We report one individual with a reciprocal translocation breakpoint within SOX5, eight individuals with intragenic SOX5 deletions (four are apparently de novo and one inherited from an affected parent), and seven individuals with larger 12p12 deletions encompassing SOX5. Common features in these subjects include prominent speech delay, intellectual disability, behavior abnormalities, and dysmorphic features. The phenotypic impact of the deletions may depend on the location of the deletion and consequently which of the three major SOX5 protein isoforms are affected. One intragenic deletion involving only untranslated exons was present in a more mildly affected subject, was inherited from a healthy parent and grandparent, and is similar to a deletion found in a control cohort. Therefore, some intragenic SOX5 deletions may have minimal phenotypic effect. Based on the location of the deletions in the subjects compared to the controls, the de novo nature of most of these deletions, and the phenotypic similarities among cases, SOX5 appears to be a dosage-sensitive, developmentally important gene

Identification de nouveaux gènes impliqués dans des maladies ophtalmologiques rares en utilisant la CGH-array

PARIS7-Bibliothèque centrale (751132105) / SudocSudocFranceF

Étude des régions sub-télomériques par MLPA chez 1041 patients présentant un retard mental non spécifique

Environ 3% de la population pédiatrique présente un retard mental (RM). La revue des cas publiés réalisée en 2003 par de Vries estime que 5% des patients présentant un RM sont porteurs d une anomalie subtélomérique. Cependant, la majorité des études rapportées ont été réalisées sur des populations de patients hautement sélectionnés cliniquement en raison de la lourdeur et du coût des kits de sondes FISH spécifiques des subtéloméres. Les objectifs de ce travail sont d établir la fréquence des microremaniements subtélomériques dans une large population de patients présentant un RM et d affiner la description des phénotypes associés à chaque microremaniement. Dans ce but, nous avons développé une stratégie de dépistage systématique des anomalies subtélomériques par une technique de PCR quantitative par MLPA (multiplex ligation dependent probe amplification). Une confirmation de l anomalie retrouvée par un second panel de sondes MLPA, puis par FISH subtélomérique a été réalisée secondairement. Cette stratégie a été appliquée à une population de 1041 patients présentant un RM de tout niveau, en s affranchissant des critères de présélection cliniques publiés qui ne nous semblaient pas satisfaisants. Un réarrangement subtélomérique a été mis en évidence par MLPA et confirmé par hybridation in situ chez 28 patients (soit 2,7%). Les résultats discordants ont été caractérisés en développant des techniques complémentaires (sondes FISH locales, PCR quantitative en temps réel). Dans un dernier temps, nous avons tenté d établir des corrélations entre le phénotype et le remaniement détecté en intégrant les données cliniques de la littérature aux observations issues de nos patientsPARIS6-Bibl.Pitié-Salpêtrie (751132101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Top-m identification for linear bandits

International audienceMotivated by an application to drug repurposing, we propose the first algorithms to tackle the identification of the m ≥ 1 arms with largest means in a linear bandit model, in the fixed-confidence setting. These algorithms belong to the generic family of Gap-Index Focused Algorithms (GIFA) that we introduce for Top-m identification in linear bandits. We propose a unified analysis of these algorithms, which shows how the use of features might decrease the sample complexity. We further validate these algorithms empirically on simulated data and on a simple drug repurposing task

Top-m identification for linear bandits

International audienceMotivated by an application to drug repurposing, we propose the first algorithms to tackle the identification of the m ≥ 1 arms with largest means in a linear bandit model, in the fixed-confidence setting. These algorithms belong to the generic family of Gap-Index Focused Algorithms (GIFA) that we introduce for Top-m identification in linear bandits. We propose a unified analysis of these algorithms, which shows how the use of features might decrease the sample complexity. We further validate these algorithms empirically on simulated data and on a simple drug repurposing task

The E148QMEFV allele is not implicated in the development of familial Mediterranean fever

International audienceFamilial Mediterranean fever (FMF) is an autosomal recessive disorder characterized by recurrent attacks of fever and serositis, common in populations of Armenian, Arab, Sephardic Jewish and Turkish origin. Early diagnosis is crucial to start colchicine therapy that prevents the occurrence of attacks and renal amyloidosis. In the absence of functional test for FMF, the diagnosis remains clinical and is generally confirmed by molecular analysis of the MEFV gene. More than 40 missense mutations and two in-frame deletions have been reported, most of them being located in exon 10 of the gene. The M694V (c.2080A>G) mutation, the most frequent defect, is responsible for a severe phenotype when present in the homozygous state. The E148Q (c.442G>C) sequence variant, which is situated in exon 2, is also common, but its role in FMF is controversial. In order to assess the implication of the E148Q variation in FMF, we investigated 233 patients of Sephardic Jewish origin living in France and 213 disease-free relatives of these patients. The frequency of the E148Q allele was found to be similar in the two groups (3.62% a nd 3.75%, respectively, p=0.93). Most importantly, the frequency of the M694V/E148Q compound heterozygous genotype was comparable between the patients group (3.9%) and the healthy relatives group (4.2%, p=0.85). This population-based study, therefore, strongly supports the hypothesis that E148Q is a just a benign polymorphism and not a disease-causing mutation. Considering this variant as a mutation may lead to set false positive diagnoses and to neglect the likely existence of genetic heterogeneity in FM

Clinical Evaluation of a Reverse Hybridization Assay for the Molecular Detection of Twelve MEFV Gene Mutations

International audienc