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The French Exome (FREX) Project : a reference panel of exomes from French regions

Novel high throughput sequencing technologies enable the characterization of all the genetic variations in the coding sequence (exome) of individuals and the discovery of novel variants involved in monogenic and complex diseases. The study of these two kinds of diseases require different methods and raises specific problems however, in both situations, the major challenge is to understand the functional role of the identified variants to filter out the neutral ones. Indeed, in each human exome, about 20,000 nucleotide variants are found among which a significant proportion is rare and not described in public databases. Filtering the candidate variants based on the information contained in public databases is difficult as these databases contain no data from France. Genome-wide association studies have shown that population stratification is a concern in Europe and even within countries in Europe. Indeed, significant allele frequency differences are seen at common SNPs and the problem is expected to be even worse at rare variants that have appeared more recently in populations and have therefore not spread over large geographic areas. Association studies on exome data could therefore considerably benefit from the setting-up of a specific database containing the exome data of a reference control panel of individuals of French ancestry. The FREX project is a federative project that aims at building such a database and at giving access to the scientific community to exome data that can serve as controls in association studies. A total of 600 individuals sampled in 6 French regions have been sequenced using the Agilent V5+UTR exome capture kit and genotyped on Illumina Core Exome SNP-chip.
The FREX consortium includes 6 partner teams :
(1) Inserm UMR 1078, UBO, EFS, CHU Brest
(2) Inserm UMR 1087, CNRS UMR 6291, l’institut du Thorax, CHU Nantes and Université de Nantes
(3) Centre National de Génotypage, Evry
(4) Inserm UMR 1079, CNR-MAJ, Rouen University Hospital, Rouen University, IRIB, Normandy University, Rouen, France
(5) Inserm UMR 1167, Institut Pasteur de Lille, Université Lille-Nord de France
(6) Inserm UMR 897, Université de Bordeaux

Publications :
G. Nicolas et al. SORL1 rare variants : a major risk factor for familial early-onset Alzheimer’s disease. Molecular Psychiatry advance online publication 25 August 2015 ; doi : 10.1038/mp.2015.121