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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.
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.
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| Label | Type | Description | Intervention Names |
|---|---|---|---|
| Ex-vivo and In-vitro approach | Other | 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 |
|
| Name | Type | Description | Arm Group Labels | Other Names |
|---|---|---|---|---|
| Ex-vivo approach concerning 25 patients | Genetic | Ex-vivo approach concerning 25 patients with blood sample in PAXgene tubes or skin biopsy and RNA-Seq analysis |
|
| Measure | Description | Time Frame |
|---|---|---|
| Proportion of VOUS reclassified as pathogenic (class 5) or benign (class 1) | 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 | Inclusion visit |
| Measure | Description | Time Frame |
|---|---|---|
| Pre-analysis process : Time of sample transport to the laboratory | 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 | Inclusion visit |
| Pre-analysis process : Quality of RNA extraction (RNA Integrity Number, RIN) |
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Inclusion Criteria:
Exclusion Criteria:
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| Name | Role | Phone | Extension | |
|---|---|---|---|---|
| Vincent MICHAUD | Contact | +335 57 82 01 93 | vincent.michaud@chu-bordeaux.fr | |
| Ndeye-Fatou NGOM | Contact | ndeye-fatou.ngom@chu-bordeaux.fr |
| Name | Affiliation | Role |
|---|---|---|
| Vincent MICHAUD | University Hospital, Bordeaux | Principal Investigator |
| Facility | Status | City | State | ZIP | Country | Contacts |
|---|---|---|---|---|---|---|
| Hopital Pellegrin | Recruiting | Bordeaux | 33000 | France |
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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.
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| In-vitro approach concerning 25 patients | Genetic | In-vitro approach concerning 25 patients without specific samples needed for analysis in minigene or luciferase assay |
|
RNA quality measurement by RIN (RNA integrity number): very good >7, good >/=5, poor <5. Only RNA with RIN >5 will be retained. |
| Inclusion visit |
| Praticability :Characteristics and number of CPU (Central Processing Unit) | Evaluation of bioinformatic ressources by measure of number of CPU needed and turnaround time for processing data | Inclusion visit |
| Praticability : Training time of Biologists for interpretation | Evaluation of training time needed to interpret the data | Inclusion visit |
| Global cost | Evaluation of cost of global analyse and each test | Inclusion visit |
| ID | Term |
|---|---|
| D008607 | Intellectual Disability |
| D012415 | Rubinstein-Taybi Syndrome |
| D003550 | Cystic Fibrosis |
| D006330 | Heart Defects, Congenital |
| D054091 | Periventricular Nodular Heterotopia |
| D006211 | Pantothenate Kinase-Associated Neurodegeneration |
| D000417 | Albinism |
| ID | Term |
|---|---|
| D019954 | Neurobehavioral Manifestations |
| D009461 | Neurologic Manifestations |
| D009422 | Nervous System Diseases |
| D012816 | Signs and Symptoms |
| D013568 | Pathological Conditions, Signs and Symptoms |
| D065886 | Neurodevelopmental Disorders |
| D001523 | Mental Disorders |
| D004413 | Dysostoses |
| D001848 | Bone Diseases, Developmental |
| D001847 | Bone Diseases |
| D009140 | Musculoskeletal Diseases |
| D019465 | Craniofacial Abnormalities |
| D009139 | Musculoskeletal Abnormalities |
| D000015 | Abnormalities, Multiple |
| D000013 | Congenital Abnormalities |
| D009358 | Congenital, Hereditary, and Neonatal Diseases and Abnormalities |
| D025063 | Chromosome Disorders |
| D030342 | Genetic Diseases, Inborn |
| D010182 | Pancreatic Diseases |
| D004066 | Digestive System Diseases |
| D008171 | Lung Diseases |
| D012140 | Respiratory Tract Diseases |
| D007232 | Infant, Newborn, Diseases |
| D018376 | Cardiovascular Abnormalities |
| D002318 | Cardiovascular Diseases |
| D006331 | Heart Diseases |
| D054081 | Malformations of Cortical Development, Group II |
| D054220 | Malformations of Cortical Development |
| D009421 | Nervous System Malformations |
| D001480 | Basal Ganglia Diseases |
| D001927 | Brain Diseases |
| D002493 | Central Nervous System Diseases |
| D019150 | Neuroaxonal Dystrophies |
| D009069 | Movement Disorders |
| D020271 | Heredodegenerative Disorders, Nervous System |
| D019636 | Neurodegenerative Diseases |
| D015785 | Eye Diseases, Hereditary |
| D005128 | Eye Diseases |
| D000592 | Amino Acid Metabolism, Inborn Errors |
| D008661 | Metabolism, Inborn Errors |
| D012873 | Skin Diseases, Genetic |
| D017496 | Hypopigmentation |
| D010859 | Pigmentation Disorders |
| D012871 | Skin Diseases |
| D017437 | Skin and Connective Tissue Diseases |
| D008659 | Metabolic Diseases |
| D009750 | Nutritional and Metabolic Diseases |
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