Systematic assessment of rare and de novo structural variants in 57 patient-parent trios using optical genome mapping

Next-generation sequencing has unraveled the genetic cause for many individuals with a rare disease, but a significant number of individuals remain undiagnosed using standard of care tests. It is anticipated that structural variants (SVs) have not been fully assessed in this context. Here, we performed optical genome mapping (OGM) for 57 trios and prioritized SVs using a two-step approach. First, we systematically identified all de novo SVs, and subsequently we studied all rare inherited SVs. Potential pathogenic SVs were confirmed using orthogonal methods. On average, we identified 6,289 SVs >500bp per proband, primarily insertions (69.8%) and deletions (27.1%). In total, we identified 13 de novo SVs, confirming a de novo mutation rate for large SVs of 0.23 or 1 in 4-5 cases. These de novo SVs impacted multiple (candidate) disease-associated genes, including NSF and FGF9. Additionally, on average per sample, we identified 11 rare inherited SVs overlapping with an established OMIM disease gene or its regulatory region, including a homozygous deletion affecting SCN9A causing congenital indifference to pain, a maternally inherited deletion in WWOX causing developmental and epileptic encephalopathy, and an interchromosomal insertion in the CMTX3 locus at Xq27.1 causing X-linked Charcot-Marie-Tooth disease. In total, we identified pathogenic SVs in three individuals and candidate disease-causing SVs in five other individuals. Overall, OGM enabled the accurate detection of challenging de novo and rare inherited SVs. Our results suggest a potential yield of disease-associated SVs in 5-14% of index cases, demonstrating that OGM can unravel previously hidden SVs in extensively tested individuals.