ObjectiveThis study is an example of the contribution of exome sequencing (ES) in selected prenatal indications, while illustrating the complexity of interpreting prenatal genetic testing. Therefore, one of the aims of this study was to better describe antenatal phenotypes.MethodsThis was a multicenter, comparative, prospective study assessing high-throughput sequencing performance (targeted gene panel versus exome sequencing) in selected prenatal indications.ResultsTrio-ES was performed on 86 fetuses, allowed making a definite etiological diagnosis in 28% of cases (24/86). One-third of diagnoses were obtained only after exome analysis (8/24, 33%). The diagnostic yield varied according to the indication and was the highest for vermian hypoplasia (5/12, 42%) and polymalformative syndromes (30%, 8/27) indications. The variants identified were mainly missense variants in ciliopathy (18%, 6/33) and cytoskeleton (15%, 5/33) genes. Among the etiological diagnoses, one fetus carried a postzygotic mosaic variant in RHOA.ConclusionIn selected indications, the diagnostic yield of ES was close to 30% and varied according to the indications, showing the importance of clearly define the malformations justifying this approach. An etiological diagnosis was made in 23 families, within a timeframe compatible with pregnancy, thus improving the management of the pregnancy and/or the unborn child.

Defects in transcription and DNA repair pathways underlie a growing spectrum of rare neurodevelopmental disorders, including MEDopathies and transcription-coupled repair (TCR)-related syndromes like Cockayne Syndrome (CS). Here, we report biallelic variants in MED20, encoding a core subunit of Mediator, in eight individuals presenting intellectual disability, brain atrophy, dystonia and developmental delay. Patient-derived fibroblasts exhibit mild but consistent defects in TCR, alongside transcriptional abnormalities reminiscent of CS. Functional modeling of MED20 variants in yeast and nematode recapitulates UV sensitivity, transcriptional impairment and neurodevelopmental defects. At the molecular level, MED20 variants disrupt interactions within the Mediator complex, disturbing the pre-initiation complex and reducing transcriptional output. Collectively, these findings identify MED20 pathogenic variants as a cause of neurodevelopmental disorder at the interface of transcription and DNA repair and position Mediator-dependent transcriptional regulation upstream of TCR. This work establishes a direct link between inherited defects in basal transcription machinery and human transcription-DNA repair syndromes.

Nuclear factor I (NFI) transcription factors regulate neural stem and progenitor differentiation during brain development. While NFIA, NFIB, and NFIX are linked to neurodevelopmental disorders, the role of NFIC (MIM: 600729) in human disease remains unclear. This study aimed to determine whether NFIC contributes to a neurodevelopmental syndrome, define its phenotype, and assess dosage-dependent effects. We established the first cohort of 11 individuals, including NFIC deletions and single nucleotide variants. Genotype-phenotype correlations, including critical region mapping, were performed. Murine data and bioinformatics were integrated to explore underlying pathomechanisms. We report 11 individuals with NFIC variants, including four with de novo SNVs and seven with deletions encompassing the gene, of whom nine have not been previously reported. A core phenotype of syndromic intellectual disability and macrocephaly was delineated. Opposing cranial phenotypes relative to proximal 19p13.3 duplication cases support a dosage-sensitive effect and a mirror-syndrome model. NFIC-related disorder represents a novel neurodevelopmental syndrome characterized by intellectual disability and macrocephaly, highlighting the importance of NFIC dosage supporting a mirror-syndrome model.

Syndromes associating both eyeball and periocular developmental anomalies, combining iris chorioretinal (ocular) coloboma and ptosis, are described in very rare clinical entities such as Baraitser-Winter cerebrofrontofacial syndrome (BWCFF). We report on six individuals from 3 unrelated families presenting with autosomal dominant eye malformations, including ocular coloboma, ptosis and craniofacial features suggesting BWCFF. However, no neurodevelopmental disorders (NDD) as usually observed in this syndrome were detected. Exome sequencing (ES) or genome sequencing (GS) was performed and allowed the identification of 3 novel heterozygous variants in the MYH10 gene, encoding the non-muscle myosin heavy chain II B. These 3 likely causative variants occur in the MYH10 tail domain required for myosin filament assembly. The MYH10 protein is mislocalized leading to abnormal actin networks in the patients’ fibroblasts compared to controls. MYH10 dysfunction leads to delayed development of the eye, as well as a muscular phenotype in the zebrafish model. Heterozygous variants in MYH10 have been recently reported to be associated with an autosomal dominant NDD with other congenital anomalies, but no patients were reported with the association of ocular coloboma and ptosis as main features. Herein, we report other MYH10 variants which cause mainly an ophthalmic phenotype without NDD expanding the phenotype associated with MYH10 and representing a differential diagnosis with BWCFF. The reason for the genotype-phenotype variability with either prominent NDD or prominent ocular features will require further investigations.

•VPS11 is associated with hypomyelinated leukodystrophy affecting children.•A single case of adult-onset generalized dystonia was reported.•We provide the first replication by describing a second case of complex dystonia related to biallelic variants in VPS11.

Résumé La cytogénétique humaine étudie la structure et la fonction des chromosomes et les corrélations entre les variations chromosomiques et le phénotype. Longtemps limitées au caryotype, les techniques d’étude des chromosomes se sont rapidement développées ces vingt dernières années. Après l’hybridation in situ en fluorescence, l’analyse chromosomique sur puce à ADN, le séquençage haut- débit short-read et long-read et la cartographie optique ont enrichi l’arsenal diagnostique du cytogénéticien. Il est à présent possible de détecter des variations chromosomiques de nombre et de structure, équilibrées ou déséquilibrées, d’une taille de plusieurs mégabases à seulement quelques dizaines de paires de bases. Ces techniques sont mises en œuvres en diagnostic prénatal, notamment en cas de signes d’appel échographiques, et en contexte postnatal dans des situations variées, allant des anomalies du développement aux troubles de la reproduction.

Protein arginine methyltransferase 9 (PRMT9) is part of the PRMT family, and it is suspected to function in pathways relevant to neurodevelopment. It is thought to participate in alternative splicing through interactions with the splicing factor SF3B2 (SAP145). In this study, we report 26 families (35 individuals) with bi-allelic loss-of-function variants in PRMT9, implicating PRMT9 in an autosomal-recessive human disease. Individuals primarily present with a neurodevelopmental disorder characterized by global developmental delay, learning disabilities, mild to severe intellectual disability, autism spectrum disorder, epilepsy, and hypotonia. The mutation spectrum includes 26 different variants such as frameshifting indels, nonsense variants, missense variants, and two copy-number variants. Mapping of the disease-causing missense variants onto the crystal structure of PRMT9 revealed that several of the variants reside within the catalytically active module of PRMT9, likely impairing its methyltransferase activity and resulting in a loss of function. In skin fibroblasts derived from affected individuals, we observed reduced expression at the RNA and/or protein level and subsequent aberrant methylation activity. Moreover, transcriptomic analysis of fibroblasts from affected individuals indicated differential expression of genes related to intellectual disability, autism, and cilia, suggesting a role of PRMT9 during ciliogenesis. Under ciliogenesis conditions, the skin-derived fibroblasts exhibited anomalies in the length of primary cilia but normal amounts of cilia. In addition, a prmt9 knockout zebrafish model displayed abnormal social preference in adult animals. Altogether, our findings implicate bi-allelic PRMT9 loss-of-function variants as causal for neurodevelopmental disorders.

BACKGROUND:Pathogenic gain-of-function or dominant-negative effect missense variations in ACTB are associated with a neurodevelopmental disorder characterised by intellectual disability (ID), seizures, sensorineural hearing loss, cerebral, renal and ocular abnormalities and dysmorphic features (Baraitser-Winter cerebrofrontofacial syndrome). ACTB encodes beta-actin, a highly conserved protein involved in cell motility, structure and integrity. Deletions including ACTB, and, more rarely, single-nucleotide loss-of-function variants in ACTB have been described in patients with a distinct phenotype including developmental delay, ID, microcephaly, growth restriction, cardiac and renal abnormalities and dysmorphic features. METHODS:We collected 14 individuals and 1 fetus carrying a heterozygous deletion including ACTB, and 4 individuals with a heterozygous truncating variant. Genotypic and phenotypic data were analysed. Furthermore, a comprehensive review of all cases reported to date was also undertaken. RESULTS:Twelve out of 17 individuals presented with ID, and 3 out of 17 with learning disabilities. Speech delay and behavioural abnormalities were observed in 15 out of 17 and 12 out of 17 individuals, respectively, motor delay in 9 out of 17 and growth restriction in 9 out of 18. Most of the individuals (13/18) had recognisable dysmorphic features. 11 anomalies were de novo, except for 1 deletion inherited from the mother. The size of the deletion varied from 125 kb to 1.6 Mb and could result from a fork stalling and template switching. CONCLUSION:This study allowed us to better characterise the phenotype associated with the haploinsufficiency of ACTB, underlying the high prevalence of neurodevelopmental disorders (ID, speech and motor delay, behavioural abnormalities) and growth restriction in this recognisable syndrome.

BACKGROUND:Genetic epilepsy diagnosis is increasing due to technological advancements. Although the use of molecular diagnosis is increasing, chromosomal microarray analysis (CMA) remains an important diagnostic tool for many patients. We aim to explore the role and indications of CMA in epilepsy, given the current genomic advances. METHODS:We obtained data from 378 epileptic described patients, who underwent CMA between 2015 and 2021. Different types of syndromic or nonsyndromic epilepsy were represented. RESULTS:After excluding patients who were undertreated or had missing data, we included 250 patients with treated epilepsy and relevant clinical information. These patients mostly had focal epilepsy or developmental and epileptic encephalopathy, with a median start age of 2 years. Ninety percent of the patients had intellectual disability, more than two thirds had normal head size, and 60% had an abnormal magnetic resonance imaging. We also included 10 patients with epilepsy without comorbidities. In our cohort, we identified 35 pathogenic copy number variations (CNVs) explaining epilepsy with nine recurrent CNVs enriched in patients with epilepsy, 12 CNVs related to neurodevelopmental disorder phenotype with possible epilepsy, five CNVs including a gene already known in epilepsy, and nine CNVs based on size combined with de novo occurrence. The diagnosis rate in our study reached 14% (35 of 250) with first-line CMA, as previously reported. Although targeted gene panel sequencing could potentially diagnose some of the reported epilepsy CNVs (34% [12 of 35]). CONCLUSIONS:CMA remains a viable option as the first-line genetic test in cases where other genetic tests are not available and as a second-line diagnostic technique if gene panel or exome sequencing yields negative results.