Year: 2025
Type: article
Study design: Observational Study
Abstract: OBJECTIVE: Approximately half of patients with hereditary myopathies remain without a definitive genetic diagnosis after DNA next-generation sequencing (NGS). Here, we implemented transcriptome analysis of muscle biopsies as a complementary diagnostic tool for patients with muscle disease but no definitive genetic diagnosis after exome sequencing. METHODS: In total, 70 undiagnosed cases with suspected genetic muscular dystrophies or congenital myopathies were included in the study. Muscle RNAseq comprised the analysis of aberrant splicing, aberrant expression, and monoallelic expression. In addition, existing NGS data or variant calling from RNAseq were reanalyzed, and genome sequencing was performed in selected cases. Four aberrant splicing open-source tools were compared and assessed. RESULTS: RNAseq established a diagnosis in 10/70 patients (14.3%) by identifying aberrant transcripts produced by single nucleotide variants (7/10) or copy number variants (3/10). Reanalysis of NGS data allowed the diagnosis in 9/70 individuals (12.9%). Based on this cohort, FRASER was the tool that reported more splicing outlier events per sample while showing the highest accuracy (81.26%). CONCLUSIONS: We demonstrate the utility of RNAseq in identifying causative variants in muscle diseases. Evaluation of four aberrant splicing tools allowed efficient identification of most pathogenic splicing events, obtaining a manageable number of candidate events for manual inspection, demonstrating feasibility for translation into a clinical setting. We also show how the integration of omic technologies reduces the turnaround time to identify causative variants.
DOI: 10.1002/acn3.70078
Authors: Alba Segarra‐Casas, Cristina Domínguez‐González, Daniel Natera‐de Benito, Solange Kapetanovic, Aurelio Hernández‐Laín, Berta Estévez‐Arias, Laura Llansó, Carlos Ortez, Cristina Jou, Itxaso Martí‐Carrera, Arístides López‐Márquez, Maria José Rodríguez, Laura González‐Mera, Velina Nedkova, Roberto Fernández‐Torrón, Benjamín Rodríguez‐Santiago, Cecília Jimenez‐Mallebrera, Raul Juntas‐Morales, Adolfo López‐de Munain, Jordi Surrallés, Andrés Nascimento, Eduard Gallardo, Montse Olivé, Pia Gallano, Lidia González‐Quereda
Institutions: Universitat Autònoma de Barcelona, Instituto de Salud Carlos III, Hospital de Sant Pau, Centre for Biomedical Network Research on Rare Diseases, Institut de Recerca Sant Pau, Hospital Sant Joan de Déu Barcelona, Institut de Recerca Sant Joan de Déu, Hospital de Basurto, Research Institute Hospital 12 de Octubre, Hospital Universitario 12 De Octubre, University of the Basque Country, Biogipuzkoa Health Research Institute, Donostiako Unibertsitate Ospitalea, Universitat de Barcelona, Bellvitge University Hospital, Institut d'Investigació Biomédica de Bellvitge, Universidad de Deusto, Biomedical Research Networking Center on Neurodegenerative Diseases, Centro de Investigación Biomédica en Red, Vall d'Hebron Hospital Universitari
Language: English
Topic: Genomics and Rare Diseases
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $4,100
Awards: Análisis integrado de datos genómicos y transcriptómicos para el avance en el conocimiento molecular y diagnóstico de las miopatías., G2050642950, Análisis del transcriptoma mediante RNA-Seq en pacientes con patología neuromuscular no resuelta tras secuenciación de exoma: optimización del algoritmo diagnóstico., G406815724, G624715701, G7363267424
OpenAlex ID: W4410718833