Zooming into rearranged genome: applying pipeline of cytological, genomic, and transcriptomic methods for structural variant interpretation

Recent advances in genomic technologies have greatly enhanced our understanding of genotype–phenotype relationships and improved diagnostic of genetic diseases. However, the dissection of complex structural variants remains challenging due to the limitations of current methods in resolving their breakpoint and interpreting phenotypes involving multiple disrupted genes. In this study, we demonstrate how an integrative approach—combining cytological, genomic, and transcriptomic methods—enables the detection, structural and functional characterization of a complex structural variants affecting the MBD5 , USP34 , and XPO1 genes. Our findings underscore the utility of the Exo-C, a modified chromosome conformation capture technique, in resolving complex rearrangements. We also report, for the first time, a composite neurodevelopmental phenotype resulting from the combined effects of MBD5 -associated intellectual disability and 2p15p16.1 microdeletion syndromes.