Abstract
<title>Abstract</title> <p> <bold>Background</bold> Neurodegenerative and neuromuscular disorders are genetically heterogeneous, and many patients remain without a genetic diagnosis after multiple rounds of clinical gene panels or exome sequencing. These approaches often fail to detect structural variants (SVs), contributing to missed diagnoses. <bold>Methods</bold> We investigated 286 individuals with neurodegenerative or neuromuscular diseases who previously received an uninformative report from diagnostic testing. Short-read genome sequencing (srGS) was used for single nucleotide variant/indel, copy number variant, and SV calling with variant prioritisation in <italic>seqr</italic> . Findings were corroborated by long-read sequencing, orthogonal validation (PCR/MLPA/Sanger), transcriptomics, and proteomics. We also assessed the utility of Talos (an automated variant prioritisation tool) to find clinically relevant SVs. <bold>Results</bold> Overall, 65/286 cases (22.7%) were solved; SVs accounted for 11/65 solved cases (16.9%). In this study, we describe 10 illustrative diagnoses spanning diverse SV classes: an intronic interspersed duplication disrupting <italic>SPAST</italic> (SPG4); SVs supporting phenotype expansions associated with <italic>SPG11</italic> , <italic>TTN</italic> , and <italic>SPTAN1;</italic> an intergenic balanced translocation downstream of <italic>FOXG1;</italic> and a pathogenic SVA insertion in <italic>TAF1</italic> detected as breakends in srGS. Talos prioritised seven of ten SV diagnoses. <bold>Conclusions</bold> SVs contribute substantially to diagnoses in neurogenetic disease cohorts and can evade panel/exome pipelines due to intronic breakpoints, balanced rearrangements, microhomology, and partial-exon events. srGS combined with automated reanalysis can shorten diagnostic timelines and improve diagnostic equity through a single, genome-wide test, although the clinical interpretation of SVs remains a significant challenge. </p>