The analysis of somatic SNVs and CNVs revealed that only few tumors harbored mutations in HLA and APP genes, while LOH due to CNVs in HLA class I and II genes occur in 5.9 to 16.7% of all cases (in HLA-A and HLA–DQA1, respectively); it reached 16.9 to 21.1% in osteosarcoma and GBM for HLA class I genes, and 20.9 to 35.7% in Ewing sarcoma and LGG for class II (DRB1-DQA1-DQB1) genes. This evidence concerns the gene APP and Ewing sarcoma.