Contribution of New Generation Oxford Nanopore-type High-throughput Sequencing in the Diagnostic Strategy of Neurogenetic Diseases.

Study Overview
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Brief Summary
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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.

Detailed Description
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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. 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.

Official Title
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Contribution of New Generation Oxford Nanopore-type High-throughput Sequencing in the Diagnostic Strategy of Neurogenetic Diseases.

Conditions
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Neuro-Degenerative Disease

Intervention / Treatment
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* Biological: Subject carrying an amplification of nucleotide repeats in one of the following 9 genes FMR1, DMPK, ZNF9, SCA2, JPH3, HD, FXN, C9ORF72, RFC1


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: minors, adults and protected adults. Subject carrying an amplification of nucleotide repeats in one of the following 9 genes FMR1, DMPK, ZNF9, SCA2, JPH3, HD, FXN, C9ORF72, RFC1 DNA available in sufficient quantity (5 to 10 µg) Exclusion Criteria: DNA degraded or of medium size <30kb, Patient objection to research - This patient objection must be reached to the center's investigator within 1 maximum period of 1 month after sending the information note.

Ages Eligible for Study
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Minimum Age: 0 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Arms and Interventions

| Intervention/Treatment |
| --- |
|Biological: Subject carrying an amplification of nucleotide repeats in one of the following 9 genes FMR1, DMPK, ZNF9, SCA2, JPH3, HD, FXN, C9ORF72, RFC1|Biological/Vaccine: DNA Samples collection as part of usual care|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | 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 | 

Secondary Outcome Measures

| Outcome Measure | 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. | through study completion, an average of 2 years |