Targeted long-read sequencing enables comprehensive analysis of the genetic and epigenetic landscape of inherited myopathies

Abstract The genetic variants that cause inherited myopathies vary widely in type, size and sequence context, encompassing small sequence variants, large structural variants, repeat expansions, and more complex events, such as the D4Z4 macrosatellite contraction and hypomethylation that causes facioscapulohumeral muscular dystrophy. Many of these are challenging to characterise using next-generation sequencing and other older molecular technologies. To address this, we developed a targeted long-read sequencing assay and bioinformatics analysis framework that captures the full suite of genes, variants and epigenetic signatures currently implicated in inherited myopathies. Applying this to a cohort of myopathy patients, we demonstrate the analytical validity of our approach and its improved accuracy and resolution compared to existing methods. Our assay led to new genetic diagnoses in 35.5% (11/31) of patients who remained undiagnosed after standard clinical genetic testing. This methodology constitutes a single streamlined assay for comprehensive genetic and epigenetic characterisation of inherited myopathies.