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Abstract
The major histocompatibility complex class I (MHC-I) genes represent the most polymorphic regions in mammalian genome. Genotyping the MHC-I is essential for determining the intracellular antigens that can be presented by MHC-I and understanding the T-cell repertoire that may recognize this peptide and MHC-I cocomplex. Software tools developed for human MHC-I genotyping do not work for canine alleles as they rely heavily on the completeness of the allele database, and the vast majority of the canine alleles remain unknown. Therefore, we developed Kmer-based paired-end read (KPR) de novo assembler and genotyper, which outperform other popular software examined in canine MHC-I genotyping. We then used this package on genotyping published paired-end RNA-seq data from 890 dogs and identified 70 new allele candidates with high confidence. We also studied the prevalent alleles in 6 major dog breeds and dog population. And we found that canine MHC-I expression is tissue related, but likely age and gender independent. New hyper-variable regions in canine MHC-I were identified for allele classification.