Whole genome and transcriptome sequencing in neuromuscular disorders: a diagnostic and health economic analysis

Background A considerable number of patients suffering from neuromuscular disorders (NMD) are unable to receive an accurate diagnosis through initial genetic testing. It is imperative to develop a cost-effective diagnostic strategy that incorporates appropriate multi-omics techniques. Methods This study included 33 NMD patients with negative results from whole-exome sequencing (WES). Whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) were performed concurrently to evaluate clinical utility. Additionally, eight diagnostic pathways were compared in terms of diagnostic rate, turnaround time, and cost. Results Our implementation of parallel WGS and RNA-seq testing successfully validated the clinical utility of this strategy in the cohort of 33 NMD patients initially yielding negative results from WES. The combined utilization of both methods resulted in an additional diagnosis for 42% (15/33) of the patients, with WGS contributing to 36% and RNA-seq contributing to 6% of the diagnoses. The Integration of alternative splicing results derived from RNA-seq data into variant filtering significantly reduced the number of rare intronic variants requiring interpretation and provided compelling evidence to support the classification of variant pathogenicity based on functional impact. Our comprehensive analysis, comparing eight different diagnostic pathways, revealed the cost-effectiveness of parallel WGS and RNA-seq testing as a diagnostic approach for patients. Moreover, the analysis of rare genomic findings within our cases showcased their potential to inform patient care, aid treatment decisions, and expand the range of NMD mutations in diagnosing rare NMD cases. Conclusion The integration of parallel WGS and RNA-seq testing represents a transformative diagnostic approach for NMD patients. The cost-effectiveness of this approach, coupled with its ability to improve diagnostic yield and interpretation efficiency, makes it a highly recommended strategy for clinical implementation to enhance the management and care of NMD patients. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study did not receive any funding ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Written informed consent was obtained from all the participants. This study was approved by the Ethics Committee of Peking Union Medical College Hospital (NO. JS-3130). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes