Panel-Based Exome Sequencing for Neuromuscular Disorders as a Diagnostic Service

Abstract

Background: Neuromuscular disorders (NMDs) are clinically and genetically heterogeneous. Accurate molecular genetic diagnosis can improve clinical management, provides appropriate genetic counseling and testing of relatives, and allows potential therapeutic trials. Objective: To establish the clinical utility of panel-based whole exome sequencing (WES) in NMDs in a population with children and adults with various neuromuscular symptoms. Methods: Clinical exome sequencing, followed by diagnostic interpretation of variants in genes associated with NMDs, was performed in a cohort of 396 patients suspected of having a genetic cause with a variable age of onset, neuromuscular phenotype, and inheritance pattern. Many had previously undergone targeted gene testing without results. Results: Disease-causing variants were identified in 75/396 patients (19%), with variants in the three COL6-genes (COL6A1, COL6A2 and COL6A3) as the most common cause of the identified muscle disorder, followed by variants in the RYR1 gene. Together, these four genes account for almost 25% of cases in whom a definite genetic cause was identified. Furthermore, likely pathogenic variants and/or variants of uncertain significance were identified in 95 of the patients (24%), in whom functional and/or segregation analysis should be used to confirm or reject the pathogenicity. In 18% of the cases with a disease-causing variant of which we received additional clinical information, we identified a genetic cause in genes of which the associated phenotypes did not match that of the patients. Hence, the advantage of panel-based WES is its unbiased approach. Conclusion: Whole exome sequencing, followed by filtering for NMD genes, offers an unbiased approach for the genetic diagnostics of NMD patients. This approach could be used as a first-tier test in neuromuscular disorders with a high suspicion of a genetic cause. With uncertain results, functional testing and segregation analysis are needed to complete the evidence.

Clinical exome sequencing in the diagnosis of pediatric neuromuscular disease

“…This is compared to a previous study done in a broader cohort of 57 general pediatric neurology patients which showed an ES diagnostic rate of 49% 19 . Our ES diagnostic rate was much higher than the diagnostic rate of 19% reported in a cohort of 396 adult NMD patients 14 . As in other studies, many of the patients presented here had clinical ES performed only after other genetic testing was performed (CMA or candidate gene testing).…”

Early-onset cerebellar ataxia in a patient with CMT2A2

“…(3) PS3, well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (performed in a research setting, so at reduced strength); (4) PM1, located in a mutational hotspot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation; (5) PM2, absent from controls; (6) PP1, cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease; and (7) PP3, multiple lines of computational evidence support a deleterious effect on the gene or gene product. Reanalysis of the WES findings by filtering for genes involved in cases of early-onset ataxia (Westra et al 2019) did not identify any other variants. We also tested for CAG repeat expansions in the coding region of 15 genes known to be associated with spinocerebellar ataxia (SCA), but these results were negative, and furthermore, most SCAs are accompanied by significant cerebellar atrophy, which was not detected in the magnetic resonance imaging (MRI) of the brain in our patient.…”

Evaluation of Laboratory Findings, Clinical Features and Rates of Diagnosis of Patients Admitted to Outpatient Clinic of Pediatric Neurology with Neuromuscular Manifestations

“…For the initial diagnosis of dystrophinopathy, the diagnostic algorithm is precisely defined, but sometimes the clinical signs, symptoms, and CK levels do not suggest a diagnosis, limiting the diagnostic rate using phenotype-driven genetic testing. Thus, for such patients, early application of NGS such as WES is recommended in neuromuscular disorders as they are likely to yield a high diagnostic rate (18,19) . We had seven patients who underwent NGS, and five of them received a diagnosis.…”