Jul 2026· Human Genetics· Vol 145· 0 citations· 83 references
Medicine
TL;DR
This study showcases the complexities and novel findings derived from a decade-long analysis of 419 Italian NDD patient-parent trios, and underscores that navigating the complexities of large NDD cohorts requires a detailed, expert-driven approach to enhance diagnostic yield.
Abstract
Exome sequencing (ES) has become a primary tool for diagnosing neurodevelopmental disorders (NDDs), yet the interpretation of genetic variants in large, heterogeneous cohorts presents significant challenges that automated pipelines often fail to resolve. This study showcases the complexities and novel findings derived from a decade-long analysis of 419 Italian NDD patient-parent trios. While ES established a molecular diagnosis in 36.5% of cases (53.8% in syndromic presentations), our investigation moves beyond diagnostic yield to highlight the critical value of manual curation integrated with deep phenotyping. We demonstrate how this rigorous approach uncovers complex disease mechanisms, revealing that variants initially misclassified as missense or stop-gain are, in fact, pathogenic splicing defects confirmed by functional analysis. Furthermore, we resolve the paradox of pathogenic truncating PPM1D variants in control databases by demonstrating their somatic mosaic nature, a crucial insight for population data interpretation. Our work also refines gene-disease correlations by challenging the established role of MID2 in NDDs, providing further evidence for DSCAM as a high-confidence risk gene, and expanding the known phenotypic spectrum of disorders, such as a novel GNAI2-related syndrome lacking expected immune dysfunction. This study underscores that navigating the complexities of large NDD cohorts requires a detailed, expert-driven approach to not only enhance diagnostic yield but also to advance our fundamental understanding of rare disease genetics.
This study provides the first systematic, mutational-level characterization of a Cypriot Mendelian disease cohort, establishing a local baseline diagnostic yield and revealing a high proportion of novel variants that reflect the underrepresentation of Eastern Mediterranean populations in global databases.
A. Theodosiou, L. Kousoulidou, Ioannis Papaevripidou et al.· Genes· 0 citations
In FTD and ALS, these results support universal access to genetic testing independent of age at onset or family history, and provide a clear diagnostic advantage in NDDs marked by substantial clinical and genetic overlap.
Emma Ehn, H. Thonberg, Inger Nennesmo et al.· Human Molecular Genetics· 0 citations
CASK-related disorders may present with severe neurodevelopmental impairment and cerebral palsy–like phenotypes, even in the absence of characteristic neuroimaging findings, which should raise suspicion for CASK-related disorders.
I. Pacheva, Elena Timova, T. Todorov et al.· Frontiers in Psychiatry· 0 citations
Functional neuronal networks are essential for brain growth and development, with myelin or "white matter" playing a key role not just in neuronal transmission but also in axonal support, maintenance, and repair. Disruption of these networks through genetic variation contributes to a range of neurodevelopmental disorders, including both primary inherited white matter disorders and an ever increasing list of secondary leukodystrophies or leucoencephalopathies. Traditionally identified using neuroimaging techniques such as magnetic resonance imaging (MRI), clinico-radiological heterogeneity means MRI alone is rarely sufficient in providing a diagnosis requiring integration with genomic techniques and expert medical review. In this study, we describe an exome-first approach in a cohort of 78 consanguineous families with undiagnosed neurodevelopmental disorders in a healthcare resource-poor setting. The aim is to demonstrate that, even in the absence of MRI imaging, we have the potential to improve diagnostic accuracy and yield. We report positive findings in six families, including known variants in MLC1, AIMP1, ASPA, and DEGS1, and novel variants in XPA and POLR3B. This study highlights the effectiveness of whole-exome sequencing as a diagnostic tool for heterogeneous neurological disorders and provides additional evidence supporting gene-disease associations in conditions linked to white matter pathology.
N. Ahmad, T. Aleem, Chunyu Liu et al.· European Journal of Human Ge...· 0 citations
Despite substantial advances in genomic testing, many individuals with neurodevelopmental disorders remain without a molecular diagnosis, while others receive a genetic diagnosis that does not fully explain phenotypic variability, developmental trajectory or tissue-specific consequences. Artificial intelligence (AI)-assisted methods are increasingly used for phenotyping, variant prioritisation, splice prediction, protein modelling, DNA methylation episignature classification and multi-omic analysis. However, these approaches differ substantially in evidentiary status and are often applied as separate prediction tasks rather than as components of an explicit mechanistic model. In this targeted narrative review, focused primarily on rare and genetically enriched neurodevelopmental disorders, we examine how AI-assisted methods may contribute to systems-level interpretation while remaining anchored to established molecular diagnosis and variant-classification frameworks. We propose a hypothesis-generating load-capacity framework comprising regulatory load, network capacity, developmental buffering and regulatory network instability. These are treated as operationalisable but currently unvalidated constructs. Regulatory instability is distinguished from stable disease-associated dysregulation, and threshold-like behaviour is presented as an empirical possibility rather than an assumed property of neurodevelopmental disease. We formulate five falsifiable predictions, consider how genomic, transcriptomic, epigenomic, single-cell, spatial, imaging, neurophysiological and longitudinal phenotypic evidence can provide complementary mechanistic constraints, and outline an auditable workflow following nondiagnostic genomic testing. We distinguish clinically implemented approaches from translational, emerging and conceptual applications, and emphasise calibration, evidence traceability, domain validity, prospective validation and appropriate abstention. Finally, we describe the Instability Twin as a prospective architecture composed of independently testable patient-specific sub-models rather than an existing clinical platform. The central proposition is that systems neurogenomics should be evaluated by whether mechanistically constrained integration provides reproducible information beyond established gene-level and simpler multimodal approaches.
Himanshu Goel, Tracy Dudding-Byth, Benjamin Kamien· Genes· 0 citations