Genome sequencing improves diagnostic outcomes over panel and exome sequencings in myopathies: findings from the French PFMG2025 initiative

Background Myopathies represent a very heterogeneous group of disease with multiple underlying causes, challenging for molecular genetic diagnosis. Hence, the diagnostic yield is very variable within the different myopathy subtypes. Current diagnostic strategies mainly rely on gene-panel or exome sequencing (ES) approaches, but they remain limited by the lack of analysis of deep intronic regions. In this study, we evaluated the diagnostic performance of a Genome Sequencing (GS) strategy for cases that were previously unresolved by gene-panel or ES in the context of myopathy diagnosis, as part of a large national scale GS strategy piloted by the French Genomic Medicine Initiative (PFMG2025). Methods Two hundred and sixty-five patients with genetically undiagnosed myopathy who underwent GS analysis as part of the PFMG2025 from July 2020 to October 2024 were included in this retrospective study. Clinical, paraclinical and genetics data were collected from the two clinical GS laboratories SeqOIA (Paris, France) and AURAGEN (Lyon, France). Results The diagnostic yield of GS in this study was of 26%, corresponding to a conclusive molecular diagnosis identifying likely pathogenic (ACMG class 4) or pathogenic (ACMG class 5) variants for 68/265 families. When considering candidate variants of unknown significance (VUS) that raised a strong diagnostic hypothesis, the diagnostic yield increased to 44%. GS was necessary for the resolution of 20.5% of cases with conclusive or candidate findings, as the variant should not have been detected using other techniques. Conclusions This nationwide program for the molecular diagnosis of myopathy showed GS as a valuable and feasible approach allowing the elucidation of complex variants and the discovery of new pathogenic mechanisms. These results highlight the complex nature of neuromuscular genetic disorders and show how GS can help providing a genetic diagnosis for these conditions in a clinical practice.