Supplementary Material for: Genetic characterization of 128 Chinese individuals with neurodevelopmental disorders via whole-exome sequencing

Introduction: Neurodevelopmental disorders (NDDs) are chronic conditions marked by abnormal brain development, presenting with significant clinical heterogeneity. Early diagnosis is crucial but challenging due to the complex symptoms. Genetic factors play a dominant role in NDDs etiology. This study was to evaluate the diagnostic utility of dual-dimension whole-exome sequencing (WES) analysis in Chinese patients with NDDs and to deepen the understanding of genotype-phenotype correlations.
Methods: This study retrospectively analyzed WES data of 128 Chinese NDDs patients from Hubei Maternal and Child Health Hospital (July 2020 - March 2024) for single nucleotide variants/small insertions-deletions (SNVs/Indels) and copy number variants (CNVs). Pathway enrichment, tissue-expression analyses, and functional experiments were conducted to interpret pathogenic genes and variants of uncertain significance (VUS).
Results: The overall diagnostic rate for NDDs was 35.9% (46/128), with 28 cases confirmed by SNV/Indel analysis (30 variants in 29 genes) and 18 by CNV analysis (22 variants). Dual-dimension analysis markdly improved the diagnostic rate compared to conventional SNV/Indel analysis (35.9% vs 21.9%). Patients with multi-system abnormalities had a higher diagnostic rate (63.2% vs 31.2%). Among the 30 SNV/Indel variants, 86.7% (26) were de novo, and 70.0% (21) were novel. Recurrent pathogenic variants in ASXL3, SHANK3 and EHMT1 genes were identified. Most pathogenic genes were enriched in transcription-regulation pathways and highly expressed in the cerebellum and cerebral cortex. Functional experiments showed that the NLGN3 c.562G>A (p.G188R) hemizygous variant affects protein stability and is deleterious, aiding prenatal diagnosis and the birth of a healthy offspring.
Conclusion: Integrating CNV analysis into routine WES workflows effectively clarifies the genetic heterogeneity of NDDs, expands the gene variant spectrum, and provides a basis for NDDs prognosis assessment and precision diagnosis and treatment.