Improving the Diagnosis of Congenital Muscular Dystrophy with Next Generation Sequencing Technology

Abstract

The congenital muscular dystrophies (CMDs) are inherited disorders of skeletal muscle characterized by early onset muscle weakness and dystrophic changes on muscle biopsy. The traditional approach to diagnosis included muscle biopsy, protein-based studies of muscle specimens, and Sanger sequencing of candidate genes. The diagnostic yield was less than 25%. As Next Generation Sequencing (NGS) moves rapidly into clinical practice, this thesis evaluates the efficacy of NGS in the diagnosis of CMD, identifies new genetic causes of congenital myopathy, evaluates the cost efficacy of a NGS approach, and re-evaluates the diagnostic algorithm. 123 CMD patients were investigated with a traditional approach, yielding a genetic diagnosis in 32% of patients. Undiagnosed patients available for further testing, were investigated using NGS techniques. Of the 85 patients who presented in the last 20 years, 28 of the 51 who lacked a confirmed genetic diagnosis consented to NGS studies. This confirmed diagnoses in a further 11 patients. Using the combination of approaches, a genetic diagnosis was achieved in 51% (43/85). In the cohort three new genetic causes of disease were identified: Early onset myopathy due to variants in PYROXD1; multisystem disease, including congenital muscular dystrophy, due to variants in PIGY; and pre-synaptic congenital myasthenic syndrome due to variants in SLC18A3. The spectrum of ACTA1, CHD7 and COL1A1-related disease was expanded. A detailed cost benefit analysis was performed on a combined CMD and nemaline myopathy cohort. Compared with the traditional diagnostic algorithm, both the NMD panel and WES, had significantly increased diagnostic yields (from 46% to 75% for the NMD panel, and 79% for WES), reduced the cost per diagnosis from AUD$22,596 to AUD$5,077 for the NMD panel and AUD$7,734 for WES. This thesis supports NGS as an effective, non-invasive first-tier investigation which can be performed in patients of any age. Muscle biopsy should be reserved as a second-tier investigation for patients undiagnosed by a NGS neuromuscular gene panel. The challenge of neuromuscular genetic research now lies with families undiagnosed after first tier NGS investigations