Transcriptomic Analysis of Fibroblasts and Blood in Patients With Rare Diseases

Not Applicable

Not yet recruiting

• Conditions: Rare Genetic Disease

• Registration Number: NCT07075107
• Lead Sponsor: Assistance Publique Hopitaux De Marseille

Brief Summary

This study aims to answer a key question in the field of rare genetic diseases by determining the prevalence of deleterious variants at RNA level in undiagnosed patients with intellectual disability and/or neonatal hypotonia. This study will put an end to diagnostic erraticism in a number of patients.

Finally, the results of this study will make it possible to compare the two types of tissue used for RNAseq, with a view to facilitating the implementation of this analysis method in the diagnostic setting.

Detailed Description

Rationale:

The majority of patients with intellectual disability or neonatal hypotonia remain undiagnosed, despite extensive genetic testing. In fact, standard analyses aimed at detecting abnormalities in the patient's DNA only enable a diagnosis to be made in a third of cases. Our hypothesis is that a certain number of these misdiagnosed patients carry anomalies (pathogenic variants) disrupting the RNA (transcript), which were not identified by DNA sequencing.

This study aims to answer a key question in the field of rare genetic diseases by determining the prevalence of deleterious variants at RNA level in undiagnosed patients with intellectual disability and/or neonatal hypotonia. This study will put an end to diagnostic erraticism in a number of patients.

Finally, the results of this study will make it possible to compare the two types of tissue used for RNAseq, with a view to facilitating the implementation of this analysis method in the diagnostic setting.

Objectives:

Determine the prevalence of variants with a deleterious effect at RNA level, identified by transcriptomic analysis (RNAseq) in diagnostically errant patients with neonatal hypotonia and/or intellectual disability. This analysis will be carried out in parallel on blood and fibroblast culture (skin biopsy).

Compare the number of pathogenic variants identified by RNAseq on blood tissue with the number of pathogenic variants identified by RNAseq on fibroblast culture. The result will help to decide whether a single sample is sufficient to obtain a diagnosis in patients in diagnostic limbo.

Study endpoints:

The number of patients initially in diagnostic errancy in whom a deleterious variant at RNA level was identified by transcriptomic analysis (RNAseq).

The number of deleterious RNA variants identified in patients in diagnostic errancy using ARNseq on fibroblasts and the deleterious RNA variants identified using ARNseq on blood samples.

Study design:

Multicentric descriptive prevalence study

Study Procedures:

Patients (or their parents in the case of minors) will be informed of the possibility of participating in the study during a follow-up consultation as part of their usual care. Patients will also be given a leaflet explaining the study. After a period of reflection, patients will be seen at one of three centers (Marseille, Toulon, Nice) to sign a consent form and take samples.

Only one visit is planned as part of the study. This is the inclusion visit, during which skin and blood samples are taken.

If a pathogenic variant explaining the phenotype is identified in a patient, the patient's physician will request confirmation of the variant by targeted analysis (Sanger sequencing) by the laboratory (Laboratoire de Génétique Moléculaire, APHM) as part of the diagnosis. This result will be provided by the patient's doctor as part of the patient's usual care.

Subjects number: 62

Study Timelines:

Inclusion period: 36 months Duration of follow-up: There is no follow-up for the patient in this study - a single inclusion visit is planned. Results will be reported as part of the patient's usual care.

Duration of analyses: 6 months Total duration (duration of inclusion and duration of analysis): 42 months

Study Timeline

• Study First Submitted: 2025-05-22
• Status Verified: 2025-07
• Study First Submitted QC: 2025-07-10
• Last Update Submitted: 2025-07-10
• Study First Posted: 2025-07-20
• Last Update Posted: 2025-07-20
• Study Start: 2025-09-01
• Primary Completion: 2029-03-01
• Study Completion: 2029-03-01

Recruitment & Eligibility

• Status: NOT_YET_RECRUITING
• Sex: All
• Target Recruitment: 62

Inclusion Criteria

• Male or female, aged 0-99 years
• Patient with neonatal intellectual disability and/or hypotonia followed at one of three inclusion centers
• Patient or parent has been informed about the study and has signed an informed consent form
• Genetic analysis by high-throughput DNA sequencing (gene panel, exome, genome) did not identify any abnormality explaining the patient's phenotype.
• If the patient's phenotype is suggestive of Prader-Willi syndrome or Angelman syndrome: a methylation anomaly test on chromosome 15 was negative.
• If the patient's phenotype is suggestive of fragile X syndrome: a repeat expansion analysis of the FMR1 gene was negative.
• If the patient's phenotype is suggestive of myotonic dystrophy type I, DM1: a repeat expansion analysis of the DMPK gene was negative.
• Patient entitled to or beneficiary of a social security scheme

Exclusion Criteria

• Patient deprived of liberty
• Pregnant or breast-feeding woman,
• The person required to sign the consent form does not understand French
• Person under guardianship and/or curatorship

Study & Design

• Study Type: INTERVENTIONAL
• Study Design: SINGLE_GROUP

Primary Outcome Measures

Name	Time	Method
Patients with identified deleterious variant at RNA level	From first enrollment to the analyse of sequencing data of the last enrolled patient.	The number of patients initially in diagnostic errancy in whom a deleterious variant at RNA level was identified by transcriptomic analysis (RNAseq).

Secondary Outcome Measures

Name	Time	Method
Comparison of the number of variants obtained from blood and from fibroblasts	From the first patient enrolled to the analyse of last enrolled patient's sequencing data	Number of deleterious RNA variants identified in patients with diagnostic errancy using ARNseq on fibroblasts and deleterious RNA variants identified using ARNseq on blood samples

Trial Locations

Locations (1)

Assistance publique - hôpitaux de Marseille; 🇫🇷 Marseille, Provence-Alpes-Côt-d'Azue, France