Elucidating the pathogenic mechanism of a pedigree with complex rearrangements on chromosome 4 using optical genome mapping technology: a study on the genetics and functional pathways in a child with developmental delay.

INTRODUCTION: Chromosomal structural variations (SVs) are important causes of neurodevelopmental disorders in children, but traditional detection techniques often fail to accurately resolve the precise breakpoints and pathogenic genes of complex rearrangements. To apply optical genome mapping (OGM) detects SVs across the whole genome by high-throughput labeling of ultra-long (>150 kb) DNA molecules, high-resolution fluorescence imaging, and alignment algorithms using a reference genome. Its resolution is up to 500 bp and is especially effective in finding exact breakpoints and orientations of complex rearrangements. This provides unprecedented technical support for clinical diagnosis and research. To perform genetic analysis of a family with chromosome 4 abnormalities using optical genome mapping technology, aiming to uncover the underlying pathogenic mechanisms. By integrating functional pathway enrichment analysis, this study explores the genotype-phenotype correlation in the patient and provides a theoretical basis for clinical diagnosis and treatment. METHODS: Karyotype analysis, multicolor fluorescence in situ hybridization (M-FISH), and OGM were performed on the proband and family members. Functional enrichment analysis was conducted using Metascape and GeneMANIA. RESULTS: The results showed that OGM technology precisely located the breakpoints, revealing that the patient carried a maternally derived derivative chromosome 4 (der(4)), with three copies of the 1q31.3, 1q31.3-q41, and 1q43 segments (totaling 20.5 Mb), involving 319 genes. Metascape analysis indicated that the genes were significantly enriched in multiple biological processes and pathways, especially in immune-related pathways and nervous system development processes, with the complement activation pathway having the highest enrichment degree, with -log10(p) reaching 13.9. Genemania showed that the candidate gene network was significantly enriched in functions related to humoral immune regulation, complement system activation, and muscle structure development, with a co-expression ratio of 98.07%. CONCLUSION: OGM technology can identify complex chromosomal rearrangements that cannot be detected by conventional methods and provides molecular evidence for the familial pattern of disease. Combined with functional pathway enrichment analysis, the study proposes that disruption of the "complement-neurodevelopmental axis" may be the main cause of the proband's neurodevelopmental disorder. These findings offer family-level evidence supporting the clinical application of OGM.