Imputation of missing HLA haplotypes. The observed allelic copy numbers at heterozygous SNP sites along each candidate SNP haplotype are color-coded as indicated at the bottom. Green bars showed the SNPs that are incompatible with the patient's genotype. Case IDs and haplotype ID (HT_ID) are indicated on the left. The locations of the 500K SNPs and HLA-A, C, B, DRB1, DQB1, and DPB1 are indicated in the figure. For each allele, genomic copy numbers were imputed using the circular binary segmentation algorithm. This divided each haplotype into one or more segments having discrete mean allelic copy numbers (blue arrows on the right). The positions of breakpoints are indicated by arrowheads. Finally, the mean allelic copy number of each segment was statistically compared with that of the corresponding segment on the other haplotype using the Wilcoxon signed rank test. Missing HLA haplotypes were determined based on the result of the statistic tests. Purple and blue lines indicated the retained and missing segments, respectively, whereas the allelic status was not determined statistically for those segments shown by green lines.