Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases
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 bu...
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2025-07-01
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| Online Access: | https://doi.org/10.1002/acn3.70078 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Alba Segarra‐Casas |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-96a88e56086741e4981cda1ba16f173f |
| institution | Matheson Library |
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| language | English |
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| series | Annals of Clinical and Translational Neurology |
| spelling | doaj-art-96a88e56086741e4981cda1ba16f173f2025-07-14T10:22:37ZengWileyAnnals of Clinical and Translational Neurology2328-95032025-07-011271465147910.1002/acn3.70078Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle DiseasesAlba Segarra‐Casas0Cristina Domínguez‐González1Daniel Natera‐de Benito2Solange Kapetanovic3Aurelio Hernández‐Laín4Berta Estévez‐Arias5Laura Llansó6Carlos Ortez7Cristina Jou8Itxaso Martí‐Carrera9Arístides López‐Márquez10Maria José Rodríguez11Laura González‐Mera12Velina Nedkova13Roberto Fernández‐Torrón14Benjamín Rodríguez‐Santiago15Cecília Jimenez‐Mallebrera16Raul Juntas‐Morales17Adolfo López‐de Munain18Jordi Surrallés19Andrés Nascimento20Eduard Gallardo21Montse Olivé22Pia Gallano23Lidia González‐Quereda24Join Research Unit on Genomic Medicine Universitat Autonòma de Barcelona‐IR SANT PAU Barcelona SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainALS and Neuromuscular Unit, Department of Neurology Hospital Universitario Basurto Bilbao SpainNeuropathology Unit, imas12 Research Institute Hospital Universitario 12 de Octubre Madrid SpainNeuromuscular Unit, Department of Neurology Hospital Sant Joan de Déu Barcelona SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainDepartment of Pediatrics Donostia University Hospital San Sebastian SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainGenetics Department Institut de Recerca Sant Pau (IR SANT PAU), Hospital de la Santa Creu i Sant Pau Barcelona SpainNeuropathology Unit, Department of Pathology and Neuromuscular Unit, Department of Neurology IDIBELL‐Hospital de Bellvitge, Hospitalet de Llobregat Barcelona SpainNeuropathology Unit, Department of Pathology and Neuromuscular Unit, Department of Neurology IDIBELL‐Hospital de Bellvitge, Hospitalet de Llobregat Barcelona SpainGroup of Neuromuscular Diseases, Donostia University Hospital, Biodonostia BioGipuzkoa Health Research Institute, OSAKIDETZA Donostia‐San Sebastián SpainJoin Research Unit on Genomic Medicine Universitat Autonòma de Barcelona‐IR SANT PAU Barcelona SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainNeuromuscular Diseases Unit, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD), Department of Neurology Vall D'hebron University Hospital Barcelona SpainGroup of Neuromuscular Diseases, Donostia University Hospital, Biodonostia BioGipuzkoa Health Research Institute, OSAKIDETZA Donostia‐San Sebastián SpainJoin Research Unit on Genomic Medicine Universitat Autonòma de Barcelona‐IR SANT PAU Barcelona SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainCentre for Biomedical Network Research on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid SpainJoin Research Unit on Genomic Medicine Universitat Autonòma de Barcelona‐IR SANT PAU Barcelona SpainJoin Research Unit on Genomic Medicine Universitat Autonòma de Barcelona‐IR SANT PAU Barcelona SpainABSTRACT 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.https://doi.org/10.1002/acn3.70078alternative splicingcongenital myopathygenetic diagnosismuscular dystrophyneuromuscular diseasesRNA sequencing |
| spellingShingle | 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 Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases Annals of Clinical and Translational Neurology alternative splicing congenital myopathy genetic diagnosis muscular dystrophy neuromuscular diseases RNA sequencing |
| title | Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases |
| title_full | Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases |
| title_fullStr | Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases |
| title_full_unstemmed | Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases |
| title_short | Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases |
| title_sort | translating muscle rnaseq into the clinic for the diagnosis of muscle diseases |
| topic | alternative splicing congenital myopathy genetic diagnosis muscular dystrophy neuromuscular diseases RNA sequencing |
| url | https://doi.org/10.1002/acn3.70078 |
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