Population Genomic Diversity of France

NCT04183023 | Active Not Recruiting

• 2 other identifiers: C19-392019-A01862-55
• Study Type: observational
• Target: 10,250
• Locations: 1 country
• Sites: 1

Brief Summary

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.

Conditions

Genetics, Population

Keywords

Whole Genome Sequencing (WGS); SNP-chip; Genetic variants; Salivary DNA; General population

Outcome Measures

Primary Outcomes (1)

• Genotypes and allele frequencies of the participants

  4,000 individuals will be selected based on the places of birth of their grandparents in order to ensure a homogeneous coverage of the different geographic regions. The DNA of these 4,000 individuals will be sequenced. Genotypes and allele frequencies at the different genomic positions where variations will be observed in the POPGEN population will be computed by simple counting of their occurences in the dataset.

  Through study completion, an average of 1 year

Study Arms (1)

Single arm

There is a unique arm in which all the participants will be included. The intervention consists in the 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 a subset of 4,000 DNA 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. 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.

Genetic: Collection of a salivary sample

Interventions

Collection of a salivary sample GENETIC

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.

Single arm

Eligibility Criteria

• Age: 18 Years+
• Sex: all
• Healthy Volunteers: Yes
• Age Groups: Adult (18-64), Older Adult (65+)
• Sampling Method: Non-Probability Sample

Study Population

Participants will be recruited among CONSTANCES cohort volunteers who agreed transmission of their data and provided information about their parents and grandparent birthplaces. Among all those individuals, 15,000 will be randomly selected according the following criteria: * The place of birth of the ascendants is known and clustered in a restricted geographic area (maximum distance between birth places will be defined after analysis of their distribution in the entire dataset), * Demography distribution in metropolitan France.

You may qualify if:

• 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.

You may not qualify if:

• 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.

Sponsors & Collaborators

• Institut National de la Santé Et de la Recherche Médicale, France: lead
• Commissariat A L'energie Atomique: collaborator

Study Sites (1)

Inserm - UMR1078 GGB

Brest, France

Location

Biospecimen

Retention: SAMPLES WITH DNA

DNA extracted from salivary samples obtained by self-collection devices

Study Officials

• Emmanuelle GENIN, Researcher

  Inserm - UMR1078 GGB

  STUDY DIRECTOR

Study Design

• Study Type: observational
• Observational Model: ECOLOGIC OR COMMUNITY
• Time Perspective: PROSPECTIVE
• Sponsor Type: OTHER GOV
• Responsible Party: SPONSOR

Study Record Dates

• First Submitted: November 14, 2019
• First Posted: December 3, 2019
• Study Start: March 31, 2021
• Primary Completion: February 19, 2022
• Study Completion (Estimated): March 31, 2031
• Last Updated: March 31, 2026

Record last verified: 2026-03

Locations

FR (1)