HLA-C and neoplasm: As a consistency check, we verified that gene-specific quantification levels obtained with arcasHLA-quant by summing minor and major allele expression for each HLA-I gene (HLA-A, HLA-B, and HLA-C) were consistent with expression levels as inferred through alternate methods [36] available on the TCGA portal (Pearson’s correlation coefficients in the range 0.94–0.96, p < 10−16 across tumor subtypes, Additional file 1: Fig. S1).