Albinism, Congenital Heart Defect, Cystic Fibrosis, Intellectual Disability, Neurodegeneration With Brain Iron Accumulation (NBIA), Periventricular Nodular Heterotopia, Rubinstein-Taybi Syndrome
Conditions
Keywords
Variant of unknown significance, Functional genetics, Translational research, RNAseq, Gene expression regulation
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.
Interventions
GENETICEx-vivo approach concerning 25 patients
Ex-vivo approach concerning 25 patients with blood sample in PAXgene tubes or skin biopsy and RNA-Seq analysis
GENETICIn-vitro approach concerning 25 patients
In-vitro approach concerning 25 patients without specific samples needed for analysis in minigene or luciferase assay
Sponsors
University Hospital, Bordeaux
Study design
Allocation
NA
Intervention model
SINGLE_GROUP
Primary purpose
DIAGNOSTIC
Masking
NONE
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.
Eligibility
Sex/Gender
ALL
Healthy volunteers
No
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
Design outcomes
Primary
| Measure | Time frame | Description |
|---|---|---|
| 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
| Measure | Time frame | Description |
|---|---|---|
| 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 |
Countries
France
Contacts
Primary ContactVincent MICHAUD
Backup ContactNdeye-Fatou NGOM
Outcome results
None listed