Development of Targeted RNA-Seq for Amyotrophic Lateral Sclerosis Diagnosis

Status: Recruiting
Location: See all (7) locations...
Intervention Type: Other
Study Type: Observational
SUMMARY

Genetic diagnosis of Amyotrophic Lateral Sclerosis (ALS) could identify the origin of the disease, potentially allowing the patient to pursue targeted/gene therapy. However, many familial forms of ALS are genetically undiagnosed, either because no variant has been detected in the genes of interest, or because the detected variant(s) have uncertain significance. Currently, molecular diagnosis takes place in two stages: 1) Search for the GGGGCC expansion in the C9ORF72 gene by RP-PCR; 2) Analysis of the coding regions by high-throughput sequencing of a panel of 30 genes involved in ALS. Many of these variants of uncertain significance affect splicing. Their impact can be predicted using in silico tools, but only an analysis of the patient's RNA can confirm their pathogenic nature. Currently, the analysis of transcripts is only done a posteriori, when a variant predicted to impact splicing is detected on the patient's DNA. RT-PCR followed by Sanger sequencing then verifies the impact of the splice variants. This method confirmed the impact of certain splice variants in patients. However, this method is time-consuming and requires custom development, and is mutation/gene/patient-dependent. In contrast, high-throughput RNA sequencing (RNA-Seq) simultaneously analyzes the splicing of numerous genes, with a global approach, applicable to all patients. This approach avoids the custom design of primers, which can be biased by the interpretation of splicing predictions, while RNA-Seq systematically captures and sequences all the transcripts. Finally, RNA-Seq provides additional information compared to DNA sequencing such as the detection of exon skipping, intron inclusion, and the creation of fusion transcripts. In the GTEx project (GTEx Consortium, 2013), expression levels of human genome transcripts were quantified by RNA-Seq. Using these results, the study investigators measured expression of transcripts of known ALS genes in whole blood. Applying a threshold value of 0.5 transcripts per million reads (TPM), 25 of the 30 ALS genes currently analyzed by NGS in routine diagnostics at Nîmes University Hospital could be eligible for a complete analysis by RNA-Seq. None of the French laboratories carrying out genetic analyzes of ALS has yet developed RNA-Seq as a routine diagnostic tool. The study laboratory receives more than 600 requests for genetic diagnosis of ALS patients per year. The aim of this study is therefore to develop a global method for analyzing RNA transcripts of ALS genes to categorize the mutations to improve the diagnostic management of patients.

Eligibility
Participation Requirements
Sex: All
Minimum Age: 18
Healthy Volunteers: f
View:

• Have a prescription for a genetic diagnosis of ALS (or familial hypercholesterolemia for the control cohort)

• Have given their informed consent for the genetic study and the biobank

• The patient must be a member or beneficiary of a health insurance plan

Locations
Other Locations
France
CHU de Bordeaux
RECRUITING
Bordeaux
CHU de Clermont-Ferrand
RECRUITING
Clermont-ferrand
CHU de Lyon
RECRUITING
Lyon
La Timone
RECRUITING
Marseille
CHU de Montpellier
RECRUITING
Montpellier
CHU de Nîmes
RECRUITING
Nîmes
CHU de Toulouse
RECRUITING
Toulouse
Contact Information
Primary
Claire Guissart
claire.guissart@chu-nimes.fr
04 66 68 32 07
Time Frame
Start Date: 2023-11-22
Estimated Completion Date: 2027-05
Participants
Target number of participants: 192
Treatments
Positive controls
6 patients already in database. The 6 confirmed splicing mutations are: DCTN1 (NM\_004082.5): c.3209G\>T, OPTN (NM\_001008211.1) : c.1613-7T\>G, FUS (NM\_004960.4) : c.764+8T\>A, GRN (NM\_002087.4): c.835+1G\>A, GRN (NM\_002087.4): c.709-3C\>G, SPG11 (NM\_025137.4): c.3039-5T\>G
Negative controls
30 patients with familial hypercholesterolemia. The absence of splicing anomalies in the SLA genes after confirmation by RT-PCR followed by Sanger sequencing of the absence of anomalies for the 6 variants listed above for each of the 30 individuals.
Exploratory cohort
156 ALS: 20 ALS patients with splice variants predicted to be deleterious by in silico prediction software; 136 panel-analysis-negative ALS patients (priority will be given to familial ALS)
Sponsors
Leads: Centre Hospitalier Universitaire de Nīmes
Collaborators: Association pour la Recherche sur la Sclérose Latérale Amyotrophique et autres maladies du motoneurones

This content was sourced from clinicaltrials.gov