SNP-HLA reference project
Project leaders: Nicolas Vince & Pierre-Antoine Gourraud.
HLA imputation from SNPs is a powerful statistical alternative from expensive NGS HLA typing. While extensive studies using SNPs genotypes grew extremely fast, much work is still needed to increase capacities of studying HLA alleles and their association with different diseases. To fill this gap between genomic data availability and HLA alleles studies, we propose to facilitate the HLA imputation from SNP studies by developing the SNP-HLA reference consortium. The SNP-HLA reference consortium main objective is to bring together immunogeneticists and other scientists in order to:
- build several large reference panels for HLA imputation from SNPs genotypes
- share these reference panels within a publicly available database.
Indeed, imputation accuracy is dependent of the reference panel quality, as well as to the matching of the queried data (e.g. ancestry background or genomic array coverage). We already have access to large cohorts of over 4,000 ethnically diverse individuals with HLA types and SNPs genotypes. We offer to provide to the consortium our own reference panels and the logistics, including an access to a high-computing infrastructure that is necessary for the reference panel building. As an example, only for HLA-A, it took 2,700 CPU-hrs for 917 individuals with 49 alleles and 5,780 SNPs to build a reference panel using HIBAG. As the reference panel bagging with the HIBAG R package uses bootstrap sampling, all the dataset will be anonymized and can therefore be released in a public database. To develop this very ambitious tool, we encourage willing participants with large HLA types + SNPs data to join the project and contribute to the development of a consortium that will empower the immunogenetic community to shift in the immunogenomic association era.