The sample ESCA_B has the lowest sequencing mean coverage (normal exome 21.73× and tumor exome 25.88×, Data Supplement, Fig S1F), but the HLA typing results are consistent across tools except one mismatch (HLA-A, ATHLATES) and other two mismatches because of loss of heterozygosity (LOH) as an effect of chromosome 6 copy loss (HLA-B, HLA-C by Polysolver; Fig 2). The gene discussed is HLA-A; the disease is neoplasm.