From Exome to Optical Mapping: Resolving a Complex 17q12 Rearrangement Underlying a Severe Neurodevelopmental...

Background Complex genomic rearrangements (CGRs) are significant contributors to neurodevelopmental disorders, yet their full structural architecture often eludes conventional diagnostic methods. We investigated the genetic basis of a 7-year-old boy presenting with severe intellectual and growth delay, immune deficiency, and multiple congenital anomalies. Methods We combined exome sequencing, array comparative genomic hybridization, short-read and long-read genome sequencing, droplet digital PCR, and optical genome mapping to characterize a chromosomal rearrangement identified in the proband and to assess segregation within the family trio. Results This integrated approach reconstructed the architecture of a highly complex duplication-triplication-quadruplication rearrangement on chromosome 17q12, encompassing the developmental and immune-regulatory genes DUSP14 , SYNRG , DDX52 , and HNF1B , consistent with the proband's phenotypic spectrum. Breakpoint mapping revealed microhomologies and inverted repeats, implicating a replication-based mechanism, such as microhomology-mediated break-induced replication, in the rearrangement's formation. Droplet digital PCR further uncovered low-level mosaicism in the asymptomatic father, indicating a potential germline transmission pathway relevant to familial recurrence risk. Conclusions Integrating multiple sequencing and optical mapping technologies can resolve complex structural variation, uncover parental mosaicism, and implicate candidate genes that conventional methods alone would miss. This approach improves molecular diagnosis and advances understanding of the mutational mechanisms underlying complex disease-associated rearrangements.