Genome-wide genotype data in the Milieu Intérieur cohort

To identify the effects of genetic factors on variation in the immune measurements, we performed genome-wide DNA genotyping of 1000 healthy adults from the Milieu Intérieur cohort. SNP array-based genotype calls for (i) 663,396 SNPs and 1,000 donors (Illumina HumanOmniExpress-24 BeadChip) and (ii) 87,960 SNPs in exonic regions and 955 donors (Illumina HumanExome-12 BeadChip) were combined, to obtain 732,341 polymorphic SNPs in the 1,000 donors; 5,699,237 genotyped and imputed SNPs were obtained in the 1,000 donors, after imputation with IMPUTE2. We imputed HLA alleles from the SNP array data, using the SNP2HLA tool.
Analyzed datasets are provided in PLINK bed, bim, fam formats, including post-QC pre-imputation SNP array data, for the whole genome or the HLA locus, and the post-imputation data. Imputed HLA alleles are provided as a txt file specifically, in the form of a matrix with 956 donors as rows and 8 HLA loci as columns.