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The human leukocyte antigen (HLA) complex is the set of genes on chromosome 6 encoding proteins of the major histocompatibility complex (MHC). These genes are divided into multiple classes with similar but distinct functions. Class I genes, such as HLA-A, HLA-B, and HLA-C, are expressed in nearly all nucleated cells and are important for recognizing endogenous foreign antigens. These antigens can arise via infection or from somatic variations, such as those introduced in cancer. Class II genes, expressed on antigen-presenting cells, generally recognize exogenous foreign antigens, such as viral peptides entering the cytoplasm after apoptosis of infected cells. HLA genes are highly polymorphic, and the number of known alleles continues to grow. Accurately identifying which alleles are present in an individual is important in many areas, such as drug safety, disease susceptibility, neoantigen prediction for cancer treatment, regenerative medicine, and organ transplantation.
(Buchkovich et al., 2017) HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data. Genome Med.