Distribution of HLA alleles in malignant tissues of patients with hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most common malignancies and a leading cause of cancerrelateddeaths worldwide. Despite evident role of human leukocyte antigen (HLA) in immune detection andkilling of cancer cells, patients. HLA genotypes has not been fully characterized in HCC. The present studyaimed to investigate the distribution of HLA allele frequency in HCC patients by in Silico HLA typing usingRNA-Sequencing (RNAseq) sequence reads. We inferred the HLA genotypes across ۳۷۱ TCGA-LIHCprimary tumor samples using arcasHLA tool from input RNA sequencing data. A total of ۵۸ HLA-A, ۸۷HLA-B, ۵۲ HLA-C, ۴۱ HLA-DPB۱, ۲۷ HLA-DQA, ۴۳ HLA-DQB۱, and ۴۳ HLA-DRB۱ alleles wereidentified in the HCC population. The most frequent allele in the HLA-A, HLA-B, HLA-C, HLA-DPB۱,HLA-DQA, HLA-DQB۱, and HLA-DRB۱ loci were (A*۰۲:۰۱:۰۱, ۱۴.۵ %), (B*۰۷:۰۲:۰, ۸.۷%),(C*۰۷:۰۲:۰۱, ۱۲.۵%), (DPB۱*۰۴:۰۱:۰۱, ۲۸.۳%), (DQA۱*۰۱:۰۲:۰۱, ۱۵%), (DQB۱*۰۳:۰۱:۰۱, ۱۴.۸%), and(DRB۱*۰۷:۰۱:۰, ۱۰.۲%), respectively. HLA-B (۸۹%) and HLA-DQB۱ (۹۰%) showed the highest level ofheterozygosity. Together, our findings showed high prevalence of some HLA alleles with probable clinicalsignificance in HCC. To provide a better plan for disease prognosis and immunotherapy treatment furtherevaluations of the identified alleles, particularly in patients as well as healthy controls, is necessary.