We observed a wide range of HLA homozygosity frequencies across tumor types and subtypes, including elevated frequencies for HLA-A and -DP in neuroblastoma with MYCN-A tumors (28.6 and 35.7%, respectively), HLA-DP in neuroblastoma with 11qLOH tumors (35%), and HLA-DR and -DQ in osteosarcoma (13.2% of patients), whereas HLA-B homozygosity was not observed in patients with HGG. Here, HLA-B is linked to osteosarcoma.