Neurodevelopmental disorders (NDDs) are common conditions including clinically diverse and genetically heterogeneous diseases, such as intellectual disability, autism spectrum disorders, and epilepsy. The intricate genetic underpinnings of NDDs pose a formidable challenge, given their multifaceted genetic architecture and heterogeneous clinical presentations. This work delves into the intricate interplay between genetic variants and phenotypic manifestations in neurodevelopmental disorders, presenting a dataset curated for the Critical Assessment of Genome Interpretation (CAGI6) ID Panel Challenge. The CAGI6 competition serves as a platform for evaluating the efficacy of computational methods in predicting phenotypic outcomes from genetic data. In this study, a targeted gene panel sequencing has been used to investigate the genetic causes of NDDs in a cohort of 415 paediatric patients. We identified 60 pathogenic and 49 likely pathogenic variants in 102 individuals that accounted for 25% of NDD cases in the cohort. The most mutated genes were ANKRD11, MECP2, ARID1B, ASH1L, CHD8, KDM5C, MED12 and PTCHD1 The majority of pathogenic variants were de novo, with some inherited from mildly affected parents. Loss-of-function variants were the most common type of pathogenic variant. In silico analysis tools were used to assess the potential impact of variants on splicing and structural/functional effects of missense variants. The study highlights the challenges in variant interpretation especially in cases with atypical phenotypic manifestations. Overall, this study provides valuable insights into the genetic causes of NDDs and emphasises the importance of understanding the underlying genetic factors for accurate diagnosis, and intervention development in neurodevelopmental conditions.

BACKGROUND:Fragile X Syndrome (FXS) is a genetic disorder caused by the lack of FMRP, a crucial protein for brain development and function. FMR1 mutations are categorized into premutation and full mutation (FXSFull), with somatic mosaicism (FXSMos) modulating the FXS phenotype. Recent studies identified muscle activity alterations during gait in FXS children. This study aims to explore the relationship between these muscle activity changes and motor fibre recruitment strategies during gait in FXS children. METHODS:Fifty-four FXS children and fourteen healthy controls participated in the study. Gait trials at self-selected speeds were recorded using four synchronized cameras and a surface electromyography system that captured bilateral activity of Gastrocnemius lateralis, Tibialis anterior, Rectus and Biceps femoris muscles. The continuous wavelet transform, using the 'bump' mother wavelet, provided the percentage distribution of signal energy across nine frequency bands (50-Hz increments within a 450- to 10-Hz spectrum) and the Instantaneous MeaN Frequency (IMNF) time-frequency distribution. RESULTS:Results indicated that both FXSFull and FXSMos children exhibit a distinct fibre recruitment strategy compared to controls, with a higher percentage of total energy and elevated IMNF (p < 0.05). CONCLUSIONS:This increased reliance on fast-twitch fibres may contribute to the observed fatigability and exercise intolerance in FXS children.

Fragile X syndrome (FXS) is a genetic neurodevelopmental disorder that causes a range of developmental problems including cognitive and behavioral impairment and learning disabilities. FXS is caused by full mutations (FM) of the FMR1 gene expansions to over 200 repeats, with hypermethylation of the cytosine–guanine–guanine (CGG) tandem repeated region in its promoter, resulting in transcriptional silencing and loss of gene function. Female carriers of FM are typically less impaired than males. The Activation Ratio (AR), the fraction of the normal allele carried on the active X chromosome, is thought to play a crucial modifying role in defining phenotype severity. Here, we compare the cognitive, neuropsychological, adaptive, and behavioral profile of two FXS girls (10 and 11 years old) with seemingly identical FMR1 genotypic profile of FM but distinctive AR levels (70% vs. 30%). A multi-method protocol, combining molecular pathophysiology and phenotypical measures, parent reports, lab-based tasks, gait analyses, and eye-tracking was employed. Results showed that lower AR corresponds to worse performances in most (cognitive, neuropsychological, adaptive, behavioral, social, mathematical skills), but not all the considered areas (i.e., time perception and gait analysis). These observations underscore the importance of AR as a phenotypic modifying parameter in females affected with FXS.

Human central nervous system (CNS) development involves complex transitions from pluripotency to regionalised neural tissues. The early phases of this process are inaccessible in humans but can potentially be modelled in vitro using brain organoids, including to study neurodevelopmental disorders. However, current methods are based on post-implantation-like human pluripotent stem cells (hPSCs), which exhibit a hypermethylated state and show epigenetic memory retention. Here we developed a 3D model of human CNS development, starting from naive human induced PSCs (hiPSCs), which exhibit a hypomethylated pre-implantation-like state of pluripotency and develop into 3D neuroepithelial cysts in a timely morphogenetic continuum. Upon treatment with appropriate signalling cues, naive-derived neuroepithelial cysts can be specified toward different axial identities. Extended culture of anterior-specified organoids results in forebrain-like structures containing both dorsal and ventral neural precursors as well as mature neurons, exhibiting appropriate cellular diversity and functional properties. We applied this system to model Fragile X Syndrome (FXS), an epigenetically regulated neurodevelopmental disorder. We found that FXS patient-derived naive hiPSCs, initially demethylated at the Fmr1 locus, gradually underwent remethylation during organoid development. In addition, Fmr1 silencing started much earlier than can be detected by pre-natal analysis, and is concomitant with the development of mosaicisms. Our approach provides a new platform for studying human CNS development, including early epigenetic events and regional patterning, demonstrating the potential of naive hiPSC-derived organoids for modelling neurodevelopmental disorders with complex epigenetic regulation. ### Competing Interest Statement The authors have declared no competing interest.

Fragile X syndrome (FXS) is a genetic condition caused by the inheritance of alleles with >200 CGG repeats in the 5′ UTR of the fragile X messenger ribonucleoprotein 1 (FMR1) gene. These full mutation (FM) alleles are associated with DNA methylation and gene silencing, which result in intellectual disabilities, developmental delays, and social and behavioral issues. Mosaicism for both the size of the CGG repeat tract and the extent of its methylation is commonly observed in individuals with the FM. Mosaicism has also been reported in carriers of premutation (PM) alleles, which have 55–200 CGG repeats. PM alleles confer risk for the fragile X premutation-associated conditions (FXPAC), including FXTAS, FXPOI, and FXAND, conditions thought to be due to the toxic consequences of transcripts containing large CGG-tracts. Unmethylated FM (UFM) alleles are transcriptionally and translationally active. Thus, they produce transcripts with toxic effects. These transcripts do produce some FMRP, the encoded product of the FMR1 gene, albeit with reduced translational efficiency. As a result, mosaicism can result in a complex clinical presentation. Here, we review the concept of mosaicism in both FXS and in PM carriers, including its potential clinical significance.

Abstract Neurodevelopmental disorders (NDDs) are common conditions including clinically diverse and genetically heterogeneous diseases, such as intellectual disability, autism spectrum disorders, and epilepsy. Understanding the genetic causes of NDDs is challenging due to their complex and heterogeneous nature. In this study, a targeted gene panel sequencing has been used to investigate the genetic causes of NDDs in a cohort of 415 pediatric patients. We identified 60 pathogenic and 49 potentially pathogenic variants in 102 individuals that accounted for 25% of NDD cases in the cohort. The majority of causative variants were de novo, with some inherited from mildly affected parents. Loss-of-function variants were the most common type of causative mutation. In silico analysis tools were used to assess the potential impact of variants on splicing and structural/functional effects of missense variants. The study highlights the challenges in variant interpretation and predicting associated phenotypes. The clinical features observed in some patients were atypical for the mutations found in their genes. Overall, this study provides valuable insights into the genetic causes of NDDs and emphasizes the importance of understanding the underlying genetic factors for accurate diagnosis, prognosis, and intervention development in neurodevelopmental conditions.

Carriers of the FMR1 premutation (PM) allele are at risk of one or more clinical conditions referred to as FX premutation-associated conditions (FXPAC). Since the FMR1 gene is on the X chromosome, the activation ratio (AR) may impact the risk, age of onset, progression, and severity of these conditions. The aim of this study was to evaluate the reliability of AR measured using different approaches and to investigate potential correlations with clinical outcomes. Molecular and clinical assessments were obtained for 30 PM female participants, and AR was assessed using both Southern blot analysis (AR-Sb) and methylation PCR (AR-mPCR). Higher ARs were associated with lower FMR1 transcript levels for any given repeat length. The higher AR-Sb was significantly associated with performance, verbal, and full-scale IQ scores, confirming previous reports. However, the AR-mPCR was not significantly associated (p > 0.05) with these measures. Similarly, the odds of depression and the number of medical conditions were correlated with higher AR-Sb but not correlated with a higher AR-mPCR. This study suggests that AR-Sb may be a more reliable measure of the AR in female carriers of PM alleles. However, further studies are warranted in a larger sample size to fully evaluate the methylation status in these participants and how it may affect the clinical phenotype.

One of the main causes of inherited intellectual disability and autism spectrum disorder called Fragile X Syndrome (FXS) is the transcriptional silencing of the FMR1 gene. "Premutation" and "full mutation" are the two most common mutations of FMR1 associated with different clinical phenotypes, and somatic mosaicism can represent a strong FXS phenotype modulator [2]. Two different FMR1 allele variations characterizes mosaicism in FXS: size mosaicism and methylation mosaicism [3]. Various musculoskeletal disorders are associated with FXS: ligamentous laxity, scoliosis, flat foot, hypotonia, which justify referral for gait analysis. The present study aims at verifying the impact of both methylation and size mosaicism on FXS children gait. The presence of differences with respect to healthy and FXS individuals with full mutation gait was also investigated. After appropriate informed consent by the parents, the gait of 54 FXS children ((FX) mean(±SD) age of 10 (±3.3) years, BMI of 19.2 (±3.7) Kg/m2) and 10 controls ((CS), mean(±SD) age of 10 (±3.07) years, BMI of 20.4 (±4.5) Kg/m2) was assessed. Within the FXS group, 29 children presented full mutation ((FX-FM), 4 methylation mosaicism (FX-MET) and 8 size mosaicism (FX-DYM (4 girl and 4 boys)). Kinematics in terms of joint angles and surface electromyographic data (sEMG) were simultaneously acquired through four synchronised cameras (GoPro Hero7) and an sEMG system (FreeEmg, BTS, 1000 Hz) that collected the activity of Tibialis Anterior, Gastrocnemius Lateralis, Rectus Femoris and Biceps Femoris. From sEMG parameters, envelope peak and its occurrence within the gait cycle were computed, sagittal plane kinematics was assessed from video recordings [2]. Concerning joint angles FX-MET showed a significant increase in hip flexion angle during the whole gait cycle meanwhile both FX-MET and FX-DYM showed a statistically significant reduction of the knee flexion and an increase of the ankle extension. In the comparison between both FX-MET and FX-DYM with CS, even though no statistically significant differences were detected, alterations were detected on the envelope shapes of all muscles. Only FX-MET showed a decrease in Tibialis Anterior activity during midstance and terminal swing, accompanied by an increase in terminal stance; a decrease in Gastrocnemius Lateralis activity during midstance, and finally an increase in Biceps Femoris activity during terminal stance. Fig. 1Download : Download high-res image (166KB)Download : Download full-size image Results suggest that FX-DYM and FX-FM showed similar differences in the sEMG pattern in comparison with CS, while FX-MET displayed a pattern more similar to CS. Meanwhile, in terms of kinematics, the data showed similar alterations in FX-MET and FX-DYM with respect to CS.

Lysine-specific demethylase 5C (KDM5C) has been identified as an important chromatin remodeling gene, contributing to X-linked neurodevelopmental disorders (NDDs). The KDM5C gene, located in the Xp22 chromosomal region, encodes the H3K4me3-me2 eraser involved in neuronal plasticity and dendritic growth. Here we report 30 individuals carrying 13 novel and one previously identified KDM5C variants. Our cohort includes the first reported case of somatic mosaicism in a male carrying a KDM5C nucleotide substitution, and a dual molecular finding in a female carrying a homozygous truncating FUCA1 alteration together with a de novo KDM5C variant. With the use of next generation sequencing strategies, we detected 1 frameshift, 1 stop codon, 2 splice-site and 10 missense variants, which pathogenic role was carefully investigated by a thorough bioinformatic analysis. The pattern of X-chromosome inactivation was found to have an impact on KDM5C phenotypic expression in females of our cohort. The affected individuals of our case series manifested a neurodevelopmental condition characterized by psychomotor delay, intellectual disability with speech disorders, and behavioral features with particular disturbed sleep pattern; other observed clinical manifestations were short stature, obesity and hypertrichosis. Collectively, these findings expand the current knowledge about the pathogenic mechanisms leading to dysfunction of this important chromatin remodeling gene and contribute to a refinement of the KDM5C phenotypic spectrum.

Importance Newborn screening for Angelman syndrome (AS), Prader-Willi syndrome (PWS), and chromosome 15 duplication syndrome (Dup15q) may lead to benefit from early diagnosis and treatment. Objective To examine the feasibility of newborn screening for these chromosome 15 imprinting disorders at population scale. Design, Setting, and Participants In this diagnostic study, the validation data set for the first-tierSNRPNtest, called methylation-specific quantitative melt analysis (MS-QMA), included 109 PWS, 48 AS, 9 Dup15q, and 1190 population control newborn blood spots (NBS) and peripheral tissue samples from participants recruited from January 2000 to December 2016. The test data set included NBS samples from 16 579 infants born in 2011. Infants with an NBS identified as positive for PWS, AS, or Dup15q by the first-tier test were referred for droplet digital polymerase chain reaction, real-time polymerase chain reaction, and low-coverage whole-genome sequencing for confirmatory testing. Data analyses were conducted between February 12, 2015, and August 15, 2020. Results In the validation data set, the median age for the 77 patients with PWS was 3.00 years (IQR, 0.01-44.50 years); for the 46 patients with AS, 2.76 years (IQR, 0.028 to 49.00 years); and for the 9 patients with Dup15q, 4.00 years (IQR, 1.00 to 28.00 years). Thirty-eight patients (51.4%) in the PWS group, 20 patients (45.5%) in the AS group, and 6 patients (66.7%) in the Dup15q group who had sex reported were male. The validation data set showed MS-QMA sensitivity of 99.0% for PWS, 93.8% for AS, and 77.8% for Dup15q; specificity of 100% for PWS, AS, and Dup15q; positive predictive and negative predictive values of 100% for PWS and AS; and a positive predictive value of 87.5% and negative predictive value of 100% for Dup15q. In the test data set of NBS samples from 16 579 infants, 92 had a positive test result using a methylation ratio cut-off of 3 standard deviations from the mean. Of these patients, 2 were confirmed to have PWS; 2, AS; and 1, maternal Dup15q. With the use of more conservative PWS- and AS-specific thresholds for positive calls from the validation data set, 9 positive NBS results were identified by MS-QMA in this cohort. The 2 PWS and 2 AS calls were confirmed by second-tier testing, but the 1 Dup15q case was not confirmed. Together, these results provided prevalence estimates of 1 in 8290 for both AS and PWS and 1 in 16 579 for maternal Dup15q, with positive predictive values for first-tier testing at 67.0% for AS, 33.0% for PWS, and 44.0% for combined detection of chromosome 15 imprinting disorders for the validation data set. Conclusions and Relevance The findings of this diagnostic study suggest that it is feasible to screen for all chromosome 15 imprinting disorders usingSNRPNmethylation analysis, with 5 individuals identified with these disorders out of 16 579 infants screened.

Fragile X syndrome (FXS) is caused by pathologic expansions of the CGG repeat polymorphic region of the FMR1 gene. There are two main categories of FMR1 mutations, “premutation” and “full mutation”, that are associated with different clinical phenotypes, and somatic mosaicism can represent a strong FXS phenotype modulator. FXS is the leading cause of inherited intellectual disability and autism, and it is characterized by musculoskeletal manifestations such as flexible flat feet, joint laxity and hypotonia. The former have been associated with altered joint kinematics and muscle activity during gait. The aim of this study was to use gait analysis parameters to classify FXS children from healthy controls and, within FXS children with full mutation, to classify children with mosaicism. Seven supervised machine learning algorithms were applied to a dataset of joint kinematics and surface electromyographic signals collected on twenty FXS children and sixteen controls. Results showed that the k-NN algorithm outperformed in terms of accuracy (100%) in classifying FXS children from controls, while CN2 rule induction obtained the best accuracy (97%) in classifying FXS children with mosaicism. The proposed pipeline might be used for developing assisted decision-making systems aiming at identifying and treating the musculoskeletal alterations associated with FXS.

On 10 March 2020, in Italy, a total lockdown was put in place to limit viral transmission of COVID-19 infection as much as possible. Research on the psychological impact of the COVID-19 pandemic highlighted detrimental effects in children and their parents. However, little is known about such effects in children with neurodevelopment disorders and their caregivers. The present study investigated how the lockdown has impacted the physiological and psychological well-being of children with Fragile X-Syndrome (FXS), aged from 2 to 16 years, and their mothers. In an online survey, 48 mothers of FXS children reported their perception of self-efficacy as caregivers and, at the same time, their children's sleep habits, behavioral and emotional difficulties during, and retrospectively, before the lockdown. Results showed a general worsening of sleep quality, and increasing behavioral problems. Although mothers reported a reduction in external support, their perception of self-efficacy as caregivers did not change during the home confinement compared to the period before. Overall, the present study suggested that specific interventions to manage sleep problems, as well as specific therapeutic and social support for increasing children and mother psychological well-being, need to be in place to mitigate the long-term effects of a lockdown.