Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases
Por:
Segarra-Casas, A, Domínguez-González, C, Natera-de Benito, D, Kapetanovic, S, Hernández-Laín, A, Estévez-Arias, B, Llansó, L, Ortez, C, Jou, C, Martí-Carrera, I, López-Márquez, A, Rodríguez, MJ, González-Mera, L, Nedkova, V, Fernández-Torrón, R, Rodríguez-Santiago, B, Jimenez-Mallebrera, C, Juntas-Morales, R, López-de Munain, A, Surrallés, J, Nascimento, A, Gallardo, E, Olivé, M, Gallano, P, González-Quereda, L
Publicada:
1 jul 2025
Ahead of Print:
1 may 2025
Resumen:
ObjectiveApproximately 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.MethodsIn 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.ResultsRNAseq 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%).ConclusionsWe 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.
Filiaciones:
Segarra-Casas, A:
Univ Autonoma Barcelona IR St PAU, Join Res Unit Genom Med, Barcelona, Spain
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Genet Dept, Barcelona, Spain
Univ Autonoma Barcelona, Genet & Microbiol Dept, Bellaterra, Spain
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Domínguez-González, C:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Hosp Univ, Imas12 Res Inst, Neurol Dept, Neuromuscular Disorders Unit, Madrid, Spain
Natera-de Benito, D:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Hosp St Joan Deu, Dept Neurol, Neuromuscular Unit, Barcelona, Spain
Inst Recerca St Joan Deu, Appl Res Neuromuscular Dis, Barcelona, Spain
Kapetanovic, S:
Hosp Univ Basurto, Dept Neurol, ALS & Neuromuscular Unit, Bilbao, Spain
BioBizkaia Basque Hlth Res Inst IIS BioBizkaia, Nucl Acid Therapeut Rare Dis NAT RD, Baracaldo, Spain
Hernández-Laín, A:
Hosp Univ 12 Octubre, Imas12 Res Inst, Neuropathol Unit, Madrid, Spain
Estévez-Arias, B:
Hosp St Joan Deu, Dept Neurol, Neuromuscular Unit, Barcelona, Spain
Inst Recerca St Joan Deu, Ctr Genom Sci Med, Lab Neurogenet & Mol Med, Barcelona, Spain
Llansó, L:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Dept Neurol, Neuromuscular Dis Unit, Barcelona, Spain
Hosp Bellvitge Princeps Espanya, IDIBELL, Dept Neurol, Neuromuscular Unit, Lhospitalet De Llobregat, Barcelona, Spain
Ortez, C:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Hosp St Joan Deu, Dept Neurol, Neuromuscular Unit, Barcelona, Spain
Inst Recerca St Joan Deu, Appl Res Neuromuscular Dis, Barcelona, Spain
Jou, C:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Inst Recerca St Joan Deu, Appl Res Neuromuscular Dis, Barcelona, Spain
Hosp St Joan Deu, Dept Pathol, Barcelona, Spain
Martí-Carrera, I:
Donostia Univ Hosp, Dept Pediat, San Sebastian, Spain
BioGipuzkoa Hlth Res Inst, Pediat Grp, San Sebastian, Spain
Univ Basque Country UPV EHU, Dept Pediat, San Sebastian, Spain
López-Márquez, A:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Hosp St Joan Deu, Dept Neurol, Neuromuscular Unit, Barcelona, Spain
Inst Recerca St Joan Deu, Appl Res Neuromuscular Dis, Barcelona, Spain
Univ Barcelona, Fac Biol, Dept Genet Microbiol & Stat, Barcelona, Spain
Rodríguez, MJ:
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Genet Dept, Barcelona, Spain
González-Mera, L:
Hosp Bellvitge Princeps Espanya, IDIBELL, Dept Pathol, Neuropathol Unit, Lhospitalet De Llobregat, Barcelona, Spain
Nedkova, V:
Hosp Bellvitge Princeps Espanya, IDIBELL, Dept Pathol, Neuropathol Unit, Lhospitalet De Llobregat, Barcelona, Spain
Hosp Bellvitge Princeps Espanya, IDIBELL, Dept Neurol, Neuromuscular Unit, Lhospitalet De Llobregat, Barcelona, Spain
Fernández-Torrón, R:
Donostia Univ Hosp, BioGipuzkoa Hlth Res Inst, Grp Neuromuscular Dis, Biodonostia,OSAKIDETZA, Donostia San Sebastian, Spain
Inst Salud Carlos III, CIBERNED Ctr Invest Biomed Red Enfermedades Neurod, CIBER, CIBERNED,ISCIII, Madrid, Spain
Univ Deusto, Fac Med, Dept Internal Med, Neurosci Area, San Sebastian Bilbao, Spain
Rodríguez-Santiago, B:
Univ Autonoma Barcelona IR St PAU, Join Res Unit Genom Med, Barcelona, Spain
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Genet Dept, Barcelona, Spain
Univ Autonoma Barcelona, Genet & Microbiol Dept, Bellaterra, Spain
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Jimenez-Mallebrera, C:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Hosp St Joan Deu, Dept Neurol, Neuromuscular Unit, Barcelona, Spain
Inst Recerca St Joan Deu, Appl Res Neuromuscular Dis, Barcelona, Spain
Juntas-Morales, R:
Vall Dhebron Univ Hosp, Dept Neurol, Neuromuscular Dis Unit, European Reference Network Rare Neuromuscular Dis,, Barcelona, Spain
López-de Munain, A:
Donostia Univ Hosp, BioGipuzkoa Hlth Res Inst, Grp Neuromuscular Dis, Biodonostia,OSAKIDETZA, Donostia San Sebastian, Spain
Inst Salud Carlos III, CIBERNED Ctr Invest Biomed Red Enfermedades Neurod, CIBER, CIBERNED,ISCIII, Madrid, Spain
Univ Deusto, Fac Med, Dept Internal Med, Neurosci Area, San Sebastian Bilbao, Spain
Univ Basque Country UPV EHU, Dept Neurosci, Grp Neurosci, Donostia San Sebastian, Spain
Surrallés, J:
Univ Autonoma Barcelona IR St PAU, Join Res Unit Genom Med, Barcelona, Spain
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Genet Dept, Barcelona, Spain
Univ Autonoma Barcelona, Genet & Microbiol Dept, Bellaterra, Spain
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Nascimento, A:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Hosp St Joan Deu, Dept Neurol, Neuromuscular Unit, Barcelona, Spain
Inst Recerca St Joan Deu, Appl Res Neuromuscular Dis, Barcelona, Spain
Gallardo, E:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Dept Neurol, Neuromuscular Dis Unit, Barcelona, Spain
Olivé, M:
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Dept Neurol, Neuromuscular Dis Unit, Barcelona, Spain
Gallano, P:
Univ Autonoma Barcelona IR St PAU, Join Res Unit Genom Med, Barcelona, Spain
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Genet Dept, Barcelona, Spain
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
González-Quereda, L:
Univ Autonoma Barcelona IR St PAU, Join Res Unit Genom Med, Barcelona, Spain
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Genet Dept, Barcelona, Spain
Univ Autonoma Barcelona, Genet & Microbiol Dept, Bellaterra, Spain
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain
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