Functional Tests to Resolve Unsolved Rare Diseases. Rares.

Not Applicable

Recruiting

• Conditions: Rubinstein-Taybi Syndrome; Albinism; Cystic Fibrosis; Intellectual Disability; Congenital Heart Defect; Periventricular Nodular Heterotopia; Neurodegeneration With Brain Iron Accumulation (NBIA)
• Interventions: Genetic: Ex-vivo approach concerning 25 patients; Genetic: In-vitro approach concerning 25 patients

• Registration Number: NCT05696912
• Lead Sponsor: University Hospital, Bordeaux

Brief Summary

Rares diseases are a heterogeneous group of conditions which need important tools for diagnosis.

The use of high-throughput sequencing is able to diagnose half of the patients. For the other part it is impossible to conclude due to the presence of variants of unknown significance (VOUS). Functional analysis are needed to bring strong argument to reclassify variants as pathogenic or benign. The main objective is to evaluate the diagnosis yield of this strategy.

Detailed Description

The main objective is the improvement of the diagnosis of rare genetic diseases. The investigator lab is expert for diagnosis of some rare diseases such as neurodevelopmental disorder, albinism, cystic fibrosis and congenital heart defect. Actually with implementation of high-throughput sequencing for diagnosis, a high number of genetic variants are found and need to be interpretated. The ACMG classification is used to classify variants with argument of variant frequency, predicted effect on protein and in-silico prediction. Functional evidence is a strong argument to help classify VOUS. The investigators propose the use of RNA-Seq, minigene and luciferase assay for study of VOUS to bring argument to classify them as benign or pathogenic.

Study Timeline

• Study First Submitted: 2022-12-07
• Study First Submitted QC: 2023-01-23
• Study First Posted: 2023-01-25
• Study Start: 2023-01-30
• Status Verified: 2024-02
• Last Update Submitted: 2024-02-20
• Last Update Posted: 2024-02-21
• Primary Completion: 2025-02
• Study Completion: 2025-02

Recruitment & Eligibility

• Status: RECRUITING
• Sex: All
• Target Recruitment: 50

Inclusion Criteria

• Minor and adult patient.
• Registered for the social security system.
• Informed consent signed by patient or parent of a minor patient.
• Patient affected by one of the rare diseases studied (albinism, congenital heart defect, cystic fibrosis, neurodevelopmental disease)
• Patient bearing variants of unknown significance (VOUS)

Exclusion Criteria

• Refusal to participate in research protocol.
• Patient under administrative supervision
• Pregnant or nursing women

Study & Design

• Study Type: INTERVENTIONAL
• Study Design: SINGLE_GROUP

Arm && Interventions

Group	Intervention	Description
Ex-vivo and In-vitro approach	In-vitro approach concerning 25 patients	Ex-vivo approach concerning 25 patients with blood sample in PAXgene tubes or skin biopsy and RNA-Seq analysis. In-vitro approach concerning 25 patients without specific samples needed for analysis in minigene or luciferase assay
Ex-vivo and In-vitro approach	Ex-vivo approach concerning 25 patients	Ex-vivo approach concerning 25 patients with blood sample in PAXgene tubes or skin biopsy and RNA-Seq analysis. In-vitro approach concerning 25 patients without specific samples needed for analysis in minigene or luciferase assay

Primary Outcome Measures

Name	Time	Method
Proportion of VOUS reclassified as pathogenic (class 5) or benign (class 1)	Inclusion visit	It's the proportion of VOUS that could be definitively reclassified as pathogenic (class 5) or benign (class 1) according to the ACMG classification (Richards et al., 2015 and Appendix 1). Indeed currently only variants considered as pathogenic or probably pathogenic make it possible to confirm a diagnosis and to propose genetic offer genetic counseling to families and perform a prenatal diagnosis. This is an evaluation that will be carried out at the end of the analyses carried out

Secondary Outcome Measures

Name	Time	Method
Pre-analysis process : Time of sample transport to the laboratory	Inclusion visit	Time of transport to the laboratory. To calculate this time, the time of collection and the time of receipt by the and the time of reception by the molecular genetics technician will be recorded
Praticability :Characteristics and number of CPU (Central Processing Unit)	Inclusion visit	Evaluation of bioinformatic ressources by measure of number of CPU needed and turnaround time for processing data
Praticability : Training time of Biologists for interpretation	Inclusion visit	Evaluation of training time needed to interpret the data
Global cost	Inclusion visit	Evaluation of cost of global analyse and each test
Pre-analysis process : Quality of RNA extraction (RNA Integrity Number, RIN)	Inclusion visit	RNA quality measurement by RIN (RNA integrity number): very good \>7, good \>/=5, poor \<5. Only RNA with RIN \>5 will be retained.

Trial Locations

Locations (1)

Hopital Pellegrin; 🇫🇷 Bordeaux, France