P103 SNP-HLA reference consortium: HLA and SNP data sharing for promoting HLA centric analyses in genomics

Aim To build large panels of reference for HLA imputation from SNP genotypes including worldwide datasets. Methods Recently, the Haplotype Reference Consortium aggregated over 20 studies to create a very large reference panel of human haplotypes where ∼ 50 M genetic variants are observed from >31,500 sequenced whole genomes ( http://www.haplotype-reference-consortium.org/ ). Based on this model we propose to use worldwide datasets to set up panels of reference with the HIBAG R package which will serve for the HLA imputation. We already have access to large cohorts of over 4000 ethnically diverse individuals with HLA types and SNPs high-resolution genotypes. Results SNP based imputation of HLA alleles is now essential in the analysis of large human genomics studies. Genotype imputation improves in accuracy with increasing numbers of sequenced samples. While extensive studies using SNP genotypes grew extremely fast; much work is still needed to increase capacities of studying HLA alleles and their association with different diseases where SNP genotypes are available. To fill this gap between genomic data availability and HLA alleles studies we propose to create a validated data framework for HLA imputation: the SNP-HLA Reference Consortium. Indeed, the aim is to facilitate the HLA imputation from SNP studies and therefore improve the correlation between SNPs and HLA genotypes. We plan to make available to the community through IHIW websites large panels of references suitable to easily impute the HLA with SNPs genotyped from chip arrays. Conclusions We present this project in the framework of the HLA and Immunogenetics Workshop in San Francisco ( http://ihiws.org/ ). To develop this very ambitious tool we encourage willing participants with large HLA types +SNP data to join the project and contribute to, as seen for SNPs within the genomic community, accuracy increases when we merge data from different ancestry backgrounds.