Transcriptomic Analysis to Put an End to Misdiagnosis in Patients With Rare Muscle Diseases (ARNseq-Musc)

Since 2017, more than 250 analyses performed at the Molecular Genetics Laboratory of the Timone Enfant Hospital have yielded negative results in patients with rare genetic muscle diseases. The researchers hypothesise that some of these misdiagnosed patients carry pathogenic RNA (transcript) disrupting variants that were not identified by DNA sequencing. In fact, DNA sequencing analyses can be negative despite the presence of a pathogenic variant that disrupts RNA splicing or expression, causing a genetic disease. For this reason, RNA sequencing can provide a diagnosis in patients who have not been diagnosed by DNA sequencing, thus putting an end to diagnostic wandering. Thus, as a descriptive prevalence study, the objectives are first to determine the rate of positive diagnoses made by the RNAseq approach in patients with muscle diseases that have not yet been diagnosed, and then to identify the genomic characteristics of the pathogenic variants identified in patients by RNAseq analysis, in order to facilitate the identification of this type of variant in future patients.

50 patients will be included in this study during 2 years.

Study Overview

• Status: Recruiting
• Conditions: Muscular Dystrophy, Duchenne; Congenital Myopathy; Muscular Dystrophy, Becker; Pompe Disease (Infantile-Onset); Rare Genetic Muscle Diseases
• Intervention / Treatment: Other: ARN extraction from muscle biopsies

• Study Type: Interventional
• Enrollment (Estimated): 50
• Phase: Not Applicable

Contacts and Locations

• Study Contact: Name: Svetlana GOROKHOVA Dr; Phone Number: +33491381927; Email: promotion.interne@ap-hm.fr

Study Locations

• France
  • Marseille, France, 13005
    • Recruiting
    • Hôpital Timone
    • Contact: Svetlana GOROKHOVA Dr; Phone Number: +33491381927; Email: promotion.interne@ap-hm.fr

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Child; Adult; Older Adult
• Accepts Healthy Volunteers: No

Description

Inclusion Criteria:

• patients with rare genetic muscle diseases who have benefited from high-throughput sequencing analysis (panel of 200 genes defined by the FILNEMUS Rare Neuromuscular Disease Network) carried out at the Molecular Genetics Laboratory, Medical Genetics Department, Timone Enfant Hospital since 2017.

This criterion is necessary to limit the analysis to patients with muscular diseases among all the patients analysed by the Molecular Genetics Laboratory.

• this genetic analysis did not identify pathogenic variants explaining the patient's phenotype This criterion is necessary in order to include only patients in diagnostic error.
• a muscle biopsy of the patient is available in the Biological Resources Centre (CRB) at the AP-HM.

Exclusion Criteria:

• Patients with no muscle biopsy available in the CRB.
• Patients with an established molecular diagnosis.
• Patients for whom RNA extraction from a muscle biopsy sample did not yield RNA of sufficient quality (INR >7) will be excluded from the study. A maximum of two extraction attempts will be performed.

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Diagnostic
• Allocation: N/A
• Interventional Model: Single Group Assignment
• Masking: None (Open Label)

Number of Arms

1

Arms and Interventions

Participant Group / Arm

Intervention / Treatment

Experimental: Sequencing of RNAseq libraries; There will be no visits from participants, so we will be using samples already in the Biological Resources Centre (CRB). RNA will be extracted from muscle biopsies taken as part of the treatment. RNAseq libraries will be sequenced by the Genomics and Bioinformatics Platform (GBiM) at Marseille Medical Genetics (MMG, U1251, AMU). Sequencing will be performed in paired-end (2*100 bp) on Illumina's Novaseq 6000 system (50 million clusters per sample, 100 M paired-end reads) and then analysed by bioinformatics.

Other: ARN extraction from muscle biopsies; There will be no visits from participants, so we will be using samples already in the Biological Resources Centre (CRB). RNA will be extracted from muscle biopsies taken as part of the treatment. RNAseq libraries will be sequenced by the Genomics and Bioinformatics Platform (GBiM) at Marseille Medical Genetics (MMG, U1251, AMU). Sequencing will be performed in paired-end (2*100 bp) on Illumina's Novaseq 6000 system (50 million clusters per sample, 100 M paired-end reads) and then analysed by bioinformatics.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
rate of positive diagnoses using the RNAseq approach	to determine the rate of positive diagnoses made using the RNAseq approach in patients with muscle diseases who have not yet been diagnosed. A patient is considered to be in diagnostic limbo if DNA sequencing of 200 genes responsible for muscle diseases has not identified pathogenic variants responsible for the patient's phenotype. Investigators are going to use transcriptomic analysis (RNA sequencing) in combination with innovative bioinformatics tools to identify variants with a deleterious effect at RNA level in patients with undiagnosed muscle diseases. This will make it possible to establish a molecular diagnosis and put an end to misdiagnosis in many patients.	From enrollment to the end of study at 24 months

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Identification of genomic characteristics	identify the genomic characteristics of pathogenic variants identified by the RNAseq approach. This analysis could potentially uncover certain characteristics that are specific to this type of variant, making it possible to suggest their presence in other undiagnosed patients in the future.	From enrollment to end of study at 24 months

Collaborators and Investigators

• Sponsor: Assistance Publique Hopitaux De Marseille

Study record dates

Study Major Dates

• Study Start (Estimated): March 1, 2025
• Primary Completion (Estimated): September 1, 2026
• Study Completion (Estimated): March 1, 2027

Study Registration Dates

• First Submitted: February 13, 2025
• First Submitted That Met QC Criteria: February 17, 2025
• First Posted (Actual): March 25, 2025

Study Record Updates

• Last Update Posted (Actual): March 25, 2025
• Last Update Submitted That Met QC Criteria: February 17, 2025
• Last Verified: February 1, 2025

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Musculoskeletal Diseases; Brain Diseases; Central Nervous System Diseases; Nervous System Diseases; Neuromuscular Diseases; Metabolism, Inborn Errors; Genetic Diseases, Inborn; Metabolic Diseases; Genetic Diseases, X-Linked; Muscular Disorders, Atrophic; Carbohydrate Metabolism, Inborn Errors; Lysosomal Storage Diseases; Brain Diseases, Metabolic, Inborn; Brain Diseases, Metabolic; Lysosomal Storage Diseases, Nervous System; Glycogen Storage Disease; Muscular Dystrophies; Muscular Diseases; Muscular Dystrophy, Duchenne; Glycogen Storage Disease Type II
• Other Study ID Numbers: RCAPHM22_0420; 2024-A01079-38 (Other Identifier: RCB)

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No