Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing

Rare diseases collectively affect approximately 1 in 10 individuals, yet current genetic testing fails to identify causal variants in most cases. The study included 1,462 families (3,450 individuals) and identified diagnostic structural variants in 5.4% of cases (79 of 1,462) using short-read sequencing, with 80% of these variants detectable only by this method compared to standard cytogenetic techniques. For 96 families, long-read sequencing with methylation profiling and transcriptomic analysis was performed. Long-read sequencing revealed over 25,000 structural variants per genome, of which 63% were not captured by short-read sequencing. However, the additional diagnostic yield from long-read sequencing was only 1.04% (1 of 96 families). The results emphasize the significant impact of comprehensive structural variant discovery in rare diseases, but also demonstrate the need for more extensive annotation of the functional and clinical significance of variants accessible only through long-read sequencing.