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Since 2012, NGS sequencing of long fragments or long reads has developed in various fields of research and today presents itself as a very promising alternative solution in the analysis of repeat amplifications. The Oxford Nanopore NGS automaton offers the prospect of bringing together 1st and 2nd line analyzes of all loci potentially indicated in neurogenetics at the same time. The project aims to compare the use of this new technology with methods currently used in reference laboratories.
The main objective is to evaluate the ability of next-generation high-throughput Oxford Nanopore-type sequencing (NEURONGS3) to diagnose 9 neurogenetic diseases compared to reference protocols via PCR (+/- Southern blot).
The secondary objective is to evaluate the repeatability of the NGS (intra-sample reproducibility) analysis in the diagnosis of 8 neurogenetic diseases.
Since 2012, NGS sequencing of long fragments or long reads has developed in various fields of research and today presents itself as a very promising alternative solution in the analysis of repeat amplifications. The Oxford Nanopore NGS automaton offers the prospect of bringing together 1st and 2nd line analyzes of all loci potentially indicated in neurogenetics at the same time. The project aims to compare the use of this new technology with methods currently used in reference laboratories.
Multicenter cross-sectional early phase diagnostic study on already existing biological collections. Analyzes with the new technique (NGS) will be carried out blinded to the results obtained with the current reference algorithm based on the sequential performance of PCRs The main objective is to evaluate the ability of next-generation high-throughput Oxford Nanopore-type sequencing (NEURONGS3) to diagnose 9 neurogenetic diseases compared to reference protocols via PCR (+/- Southern blot).
The secondary objective is to evaluate the repeatability of the NGS (intra-sample reproducibility) analysis in the diagnosis of 8 neurogenetic diseases.
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| Name | Type | Description | Arm Group Labels | Other Names |
|---|---|---|---|---|
| Subject carrying an amplification of nucleotide repeats in one of the following 9 genes FMR1, DMPK, ZNF9, SCA2, JPH3, HD, FXN, C9ORF72, RFC1 | Biological | Biological/Vaccine: DNA Samples collection as part of usual care |
| Measure | Description | Time Frame |
|---|---|---|
| Proportion of patients tested positive by Next Generation Sequencing among all the patients tested positive by the current algorithm based on PCRs | For each of the 9 considered diseases, the proportion will be established as well as its 95% confidence interval. | through study completion, an average of 2 years |
| Measure | Description | Time Frame |
|---|---|---|
| Difference between the number of repetition amplifications found by the Next Generation Sequencing method and the number of repetition amplifications found by the PCR diagnosis method | For each of the 9 considered diseases, the number of repetition amplifications found by the Next Generation Sequencing method will be compared to the number of repetition amplifications found by the PCR diagnosis method using the Bland et Altman graphs. The average and standard deviation of the difference will be calculated. |
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Inclusion Criteria:
Exclusion Criteria:
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Subject carrying an amplification of nucleotide repeats in one of the following 9 genes FMR1, DMPK, ZNF9, SCA2, JPH3, HD, FXN, C9ORF72, RFC1
| Name | Role | Phone | Extension | |
|---|---|---|---|---|
| Cyril Goizet | Contact | 05 56 79 59 52 | cyril.goizet@chu-bordeaux.fr | |
| Marie-Pierre Baudier | Contact | 05 57 82 05 92 | marie-pierre.baudier@chu-bordeaux.fr |
| Name | Affiliation | Role |
|---|---|---|
| Cyril Goizet | University Hospital, Bordeaux | Principal Investigator |
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5 to 10 µg of DNA samples per patient.
| through study completion, an average of 2 years |
| ID | Term |
|---|---|
| D065636 | Myotonin-Protein Kinase |
| C433227 | CNBP protein, human |
| D053439 | Lipoproteins, HDL2 |
| D000096923 | Frataxin |
| ID | Term |
|---|---|
| D017346 | Protein Serine-Threonine Kinases |
| D011494 | Protein Kinases |
| D017853 | Phosphotransferases (Alcohol Group Acceptor) |
| D010770 | Phosphotransferases |
| D014166 | Transferases |
| D004798 | Enzymes |
| D045762 | Enzymes and Coenzymes |
| D047908 | Intracellular Signaling Peptides and Proteins |
| D011506 | Proteins |
| D000602 | Amino Acids, Peptides, and Proteins |
| D008075 | Lipoproteins, HDL |
| D008074 | Lipoproteins |
| D008055 | Lipids |
| D007506 | Iron-Sulfur Proteins |
| D019159 | Nonheme Iron Proteins |
| D033862 | Iron-Binding Proteins |
| D002352 | Carrier Proteins |
| D008667 | Metalloproteins |
| D024101 | Mitochondrial Proteins |
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