Table 1. Concordance rate between imputed and actual allele of HLA genes^a.

Allelic resolution	HLA genes
	A	B	C	DRB1	DPB1	DQB1	DRB3	DRB4	DRB5	Total
2-digit	0.970	0.916	0.970	0.892	0.966	0.954	0.919	0.959	0.979	0.947
4-digit	0.913	0.867	0.930	0.815	0.949	0.908	0.918	0.958	0.979	0.915

^a Imputation accuracy was examined by cross-validation comparing the imputed and actual genotypes of classical alleles of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DPB1, HLA-DQB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5, as described following. The Korean HLA reference panel subjects (n = 413) were randomly divided into 10 almost equal sized subgroups (n≈41). Of the 10 subgroups, a single subgroup (n≈41) is retained as the test group to be imputed for HLA variants, and the remaining 9 subgroups (n≈372) are used for an HLA reference panel. The classical HLA alleles in a test group were then imputed from MHC SNPs in the test group using SNP2HLA and the reference panel that was constructed from the matched reference group. Average concordance rates were calculated from concordance rates between imputed and actual 2-digit and 4-digit classical alleles (including deleted alleles in HLA-DRB3, HLA-DRB4, and HLA-DRB5) of each HLA gene.