Completely resolved structural variants by optical genome mapping with adaptive sampling from CNV discovery

Structural variants (SVs), including duplications, deletions, inversions, translocations, and insertions, play major roles in human phenotypic diversity but remain difficult to detect because of variable size and structural complexity. Optical genome mapping (OGM) uses ultra-high molecular weight DNA (>150 kb) fluorescently labeled at a specific six-nucleotide sequence, enabling comprehensive SV detection by analyzing labeling patterns along long DNA molecules. This study aimed to fully characterize SVs using OGM. OGM was applied to 30 cases with exome sequencing-based copy number (CN) variants (16 CN losses, 7 CN gains, and 7 combined CN losses and gains). Additionally, targeted Oxford Nanopore long-read sequencing with adaptive sampling was used to determine breakpoints of SVs. This approach revealed undetected SVs in 14 cases (46.7%), and disclosed gene disruptions or CN alterations explaining clinical features in seven cases (23.3%). Even complex SVs involving numerous chromosomal segments and breakpoints were resolved efficiently, highlighting the power of combining OGM and long-read sequencing. Integrating OGM with long-read sequencing improves diagnostic resolution beyond sequencing alone and provides a robust framework for interpreting complex SVs. These findings highlight the potential clinical utility of combining OGM and long-read sequencing as a comprehensive diagnostic strategy for improved precision medicine in rare genetic diseases.