RID: Functional Tests to Resolve Unsolved Rare Diseases. Rares.

Sponsor

University Hospital, Bordeaux (Other)

Overall Status

Not yet recruiting

CT.gov ID

NCT05696912

Collaborator

(none)

Enrollment

Location

Arm

Anticipated Duration (Months)

4.2

Patients Per Site Per Month

Study Details

Study Description

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.

Condition or Disease	Intervention/Treatment	Phase
Intellectual Disability Rubinstein-Taybi Syndrome Cystic Fibrosis Congenital Heart Defect Periventricular Nodular Heterotopia Neurodegeneration With Brain Iron Accumulation (NBIA) Albinism	Genetic: Ex-vivo approach concerning 25 patients Genetic: In-vitro approach concerning 25 patients	N/A

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 Design

Study Type:

Interventional

Anticipated Enrollment :

50 participants

Allocation:

N/A

Intervention Model:

Single Group Assignment

Intervention Model Description:

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 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.

Masking:

None (Open Label)

Primary Purpose:

Diagnostic

Official Title:

Resolving Unsolved Rare Diseases : Functional Tests and New Diagnosis Strategy to Study Genetic Variants From High-throughput Sequencing (RID)

Anticipated Study Start Date :

Feb 1, 2023

Anticipated Primary Completion Date :

Feb 1, 2024

Anticipated Study Completion Date :

Feb 1, 2024

Arms and Interventions

Arm	Intervention/Treatment
Other: Ex-vivo and In-vitro approach 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	Genetic: 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 Genetic: In-vitro approach concerning 25 patients In-vitro approach concerning 25 patients without specific samples needed for analysis in minigene or luciferase assay

Arm

Intervention/Treatment

Other: Ex-vivo and In-vitro approach

Genetic: 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

Genetic: In-vitro approach concerning 25 patients

In-vitro approach concerning 25 patients without specific samples needed for analysis in minigene or luciferase assay

Outcome Measures

Primary Outcome Measures

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

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
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.
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

Eligibility Criteria

Criteria

Ages Eligible for Study:

N/A and Older

Sexes Eligible for Study:

All

Accepts Healthy Volunteers:

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)