Benchmarking HLA genotyping and clarifying HLA impact on survival in tumor immunotherapy.

ABSTRACT: Human leukocyte antigen (HLA) genotyping gains intensive attention due to its critical role in cancer immunotherapy. It is still a challenging issue to generate reliable HLA genotyping results through in silico tools. In addition, the survival impact of HLA alleles in tumor prognosis and immunotherapy remains controversial. In this study, the benchmarking of HLA genotyping on TCGA is performed and a 'Gun-Bullet' model which helps to clarify the survival impact of HLA allele is presented. The performance of HLA class I genotyping is generally better than class II. POLYSOLVER, OptiType, and xHLA perform generally better at HLA class I calling with an accuracy of 0.954, 0.949, and 0.937, respectively. HLA-HD obtained the highest accuracy of 0.904 on HLA class II alleles calling. Each HLA geno

SUBMITTER: Li X 

PROVIDER: S-EPMC8253103 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature