Trio genome analysis in 45 unsolved children with neuromuscular diseases

Next-generation sequencing (NGS) has revolutionized the diagnosis of inherited neuromuscular diseases (NMDs), but establishing a molecular diagnosis remains a challenge in around 50% of cases. In this study, we aimed to determine the diagnostic value of combining standardized high-quality phenotyping with trio genome sequencing in unsolved NMD patients who had previously undergone gene panels or singleton WES testing. Sequencing of all trios was performed within the SolveRD project and variant analyses were performed on the GPAP platform. We established a genetic diagnosis in 14 out of 45 index patients (31%), and identified variants likely responsible for the phenotype in an additional 3 patients (7%). The highest diagnostic yield was observed in patients with myopathy (47%). The diagnostic rate in subgroups of patients with congenital myasthenia, arthrogryposis multiplex congenita, and axonal neuropathy ranged from 21% to 33%. Causal variants were identified in 10 different genes: TTN, RYR1, TRIP4, BICD2, DYNC1H1, GLDN, SLC18A3, PIEZO2, TPM3, and UBA1. In addition, variants in three patients that may lead to the discovery of new genes or new genotype-phenotype associations were identified. The reasons that had previously prevented reaching a genetic diagnosis in the 14 solved patients were (1) variants located in regions with low coverage in the previous study (36%), (2) variants located in genes that at the time of the first NGS analysis had not been linked to any human disease (29%), (3) variants located in genes that were not sequenced and/or analyzed in the previous panels (21%), (4) variants were overlooked in the previous analyses (14%). Our approach based on standardized high-quality phenotyping and trio genome sequencing was highly effective, with a diagnostic rate of 31% compared to 15% reported in studies that only performed reanalysis. Next-generation sequencing (NGS) has revolutionized the diagnosis of inherited neuromuscular diseases (NMDs), but establishing a molecular diagnosis remains a challenge in around 50% of cases. In this study, we aimed to determine the diagnostic value of combining standardized high-quality phenotyping with trio genome sequencing in unsolved NMD patients who had previously undergone gene panels or singleton WES testing. Sequencing of all trios was performed within the SolveRD project and variant analyses were performed on the GPAP platform. We established a genetic diagnosis in 14 out of 45 index patients (31%), and identified variants likely responsible for the phenotype in an additional 3 patients (7%). The highest diagnostic yield was observed in patients with myopathy (47%). The diagnostic rate in subgroups of patients with congenital myasthenia, arthrogryposis multiplex congenita, and axonal neuropathy ranged from 21% to 33%. Causal variants were identified in 10 different genes: TTN, RYR1, TRIP4, BICD2, DYNC1H1, GLDN, SLC18A3, PIEZO2, TPM3, and UBA1. In addition, variants in three patients that may lead to the discovery of new genes or new genotype-phenotype associations were identified. The reasons that had previously prevented reaching a genetic diagnosis in the 14 solved patients were (1) variants located in regions with low coverage in the previous study (36%), (2) variants located in genes that at the time of the first NGS analysis had not been linked to any human disease (29%), (3) variants located in genes that were not sequenced and/or analyzed in the previous panels (21%), (4) variants were overlooked in the previous analyses (14%). Our approach based on standardized high-quality phenotyping and trio genome sequencing was highly effective, with a diagnostic rate of 31% compared to 15% reported in studies that only performed reanalysis.