Clinical trial
Population Genomic Diversity of France
Name
C19-39
Description
Having access to DNA sequences from individuals that share common ancestry with patients is of interest when analysing individual genomes for diagnoses. Information regarding allele frequency distribution in the same geographic areas where patients have ancestry will be necessary to help select the variants that are the most likely involved in disease and should hence be tested in functional assays.
To provide such a general population panel for France, the POPGEN project will select 10,000 individuals from CONSTANCES cohort with ancestry in different regions of France outside western part. These participants will have their DNA extracted from salivary kits and genotyped using SNP-chip. Among these 10,000 individuals, 4,000 individuals will have their whole genome sequenced. This study is one of the four pilot projects of the France Genomic Medicine plan (FMG 2025). The FMG2025 plan aims at introducing genome sequencing in the routine clinical practice to accelerate and improve diagnoses. The POPGEN project will provide the required references from the general French population to help filter out common variants from the genomes of patients.
Trial arms
Trial start
2021-03-31
Estimated PCD
2022-02-19
Trial end
2031-03-31
Status
Active (not recruiting)
Treatment
Collection of a salivary sample
Volunteers who agreed to participate will have to collect their saliva with the self-collection device. They will then send back their saliva sample and a dated and signed copy of the informed consent form in the pre-paid return envelope.
All DNA of the saliva samples will be automatically extracted, then DNA samples will be genotyped and 4,000 of them will be sequenced.
The genotyping will consist of measurement of general genetic variation, including the Single Nucleotide Polymorphisms. The SNP genotyping will be carried out using Illumina high density chips, in CNRGH production platform.
A subset of 4,000 individuals will be selected to provide a homogeneous geographic coverage and to avoid inclusion of related individuals who will share large genomic regions. Sequencing will be performed in order to reach a mean coverage of 30X for each sample and a minimum of 25X mean coverage.
Finally, a bioinformatics analysis will be performed on sequencing data.
Arms:
Single arm
Size
10250
Primary endpoint
Genotypes and allele frequencies of the participants
Through study completion, an average of 1 year
Eligibility criteria
Inclusion Criteria:
* participant included in CONSTANCES Cohort and have agreed to transmit their data for research purposes,
* participant meeting the geographic criteria of the study,
* participant who has given his consent for participating to this study.
Exclusion Criteria:
* participant who do not have sent back their informed consent or the informed consent is non-complying
* participant who do not to have provided a written free informed consent, such as for individuals placed under tutorship or guardianship.
Protocol
{'studyType': 'OBSERVATIONAL', 'patientRegistry': False, 'designInfo': {'observationalModel': 'ECOLOGIC_OR_COMMUNITY', 'timePerspective': 'PROSPECTIVE'}, 'bioSpec': {'retention': 'SAMPLES_WITH_DNA', 'description': 'DNA extracted from salivary samples obtained by self-collection devices'}, 'enrollmentInfo': {'count': 10250, 'type': 'ACTUAL'}}
Updated at
2024-01-19
1 organization
1 product
2 indications
Product
Salivary sampleIndication
GeneticsIndication
population