HLA-DQβ1 amino acid position 87 and DQB1*0301 are associated with Chinese Han SLE

BACKGROUND: Several susceptibility loci have been identified associated with Chinese Han systemic lupus erythematosus (SLE). METHODS: We carried out imputation of classical HLA alleles, amino acids and Single Nucleotide Polymorphisms (SNPs) across the MHC region in Chinese Han SLE genome-wide association study (GWAS) of mainland and Hong Kong populations for the first time using newly constructed Han-MHC reference panel followed by stepwise conditional analysis. RESULTS: We mapped the most significant independent association to HLA-DQβ1 at amino acid position (Phe87, p = 7.807 × 10-17 ) and an independent association at HLA-DQB1*0301 (Pcondiational  = 1.43 × 10-7 ). CONCLUSION: Our study illustrates the value of population-specific HLA reference panel for fine-mapping causal variants in the MHC.