473P Using RNAseq analysis in a cohort of undiagnosed congenital myopathy patients

• Published in: Neuromuscular disorders : NMD Vol. 43; p. 104441
• Main Authors: Barraza-Flores, P., Genetti, C., Shao, W., French, C., Rockowitz, S., Beggs, A.
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01-10-2024
• ISSN: 0960-8966
• DOI: 10.1016/j.nmd.2024.07.319

Congenital myopathies (CM) are a group of clinically heterogenous disorders, defined by muscle histopathology, with overlapping genetic etiologies. With the advent of next generation sequencing, molecular diagnoses are achieved in most cases using gene panels, Exome Sequencing (ES) or Genome Sequencing (GS). The Beggs Laboratory CM cohort consists of 1,110 CM cases, 68% of whom have an established molecular diagnosis using genomic testing. However, a subset of patients remains undiagnosed. We hypothesize that a proportion of these unsolved cases may be due to pathogenic variants that impact splicing and/or mono-allelic expression of heterozygous variants, not identifiable with gene panel or ES/GS analyses alone. To address this, we complemented existing genomic sequencing data with RNA sequencing (RNAseq) of patient muscle biopsies. 136 cases underwent RNAseq, of which 89 were undiagnosed. The remaining 47 had mutations in known CM genes, allowing for assessment of sensitivity for detection of known pathogenic variants. The analysis aimed to identify changes in gene expression, splicing patterns, and mono-allelic expression. We used the detection of RNA outliers pipeline (DROP) bioinformatic tool which includes FRASER, OUTRIDER, and Mono Allelic Expression (MAE) modules for the study of these genetic events. Results were filtered using a comprehensive list of skeletal muscle genes and cases were individually reviewed accounting for their clinicopathological phenotype and suspected inheritance model. Here we present the range of diagnoses facilitated by RNAseq for previously unsolved cases and estimate the utility of this approach in a diagnostic setting. So far, out of 40 reviewed undiagnosed cases, 6 have been solved, 13 show a strong candidate genetic event with ongoing genomic confirmation, and 5 show alternative splicing. These results highlight the value of RNAseq as a method for diagnosing CM cases that remain unsolved following other genomic approaches.