Genetic Diversity and Haplotype Architecture of Non-Classical HLA Class I Genes in the Japanese Population

The non-classical Class I genes (HLA-E, HLA-F and HLA-G) show limited protein-level diversity; however, full-length analyses that include regulatory and noncoding regions have not been sufficiently performed in East Asian populations. We designed new primers for long-range PCR and conducted PacBio SMRT sequencing to generate full-length gene sequences of HLA-E, HLA-F and HLA-G, including 5' and 3' untranslated regions (UTRs) as well as coding and intronic regions in 531 healthy Japanese individuals. These data enabled the full phasing of HLA-E, HLA-F and HLA-G, including upstream and downstream variants, at four-field resolution. We identified 24 HLA-E alleles, 30 HLA-F alleles and 19 HLA-G alleles, including a total of 36 novel (10 HLA-E, 19 HLA-F and 7 HLA-G) and 16 extended alleles (13 HLA-E, 1 HLA-F and 2 HLA-G). Protein-level diversity for HLA-E was limited, with E*01:03 and E*01:01 predominating. For HLA-F, despite the predominance of F*01:01 (96.7%), noncoding diversity at four-field resolution was abundant; the expression-linked rs2523405-T allele phased with F*01:01:02 and F*01:01:06, as well as with a subset of F*01:01:01 sub alleles. For HLA-G, consistent with previous reports, four-field resolution alleles and UTR variants formed fully co-segregating haplotypes. Linkage disequilibrium (LD) analysis at four-field resolution showed no LD between HLA-E and either HLA-F or HLA-G, whereas moderate LD was observed between HLA-F and HLA-G; the strongest signal was driven by F*01:01:02:09, which forms a haplotype with G*01:01:03:03. In summary, full-gene long-read sequencing clarified allele frequencies of non-classical Class I genes in the Japanese population, delineated phasing in regulatory regions and refined the LD structure between HLA-F and HLA-G by resolving four-field haplotypes. These data constitute an important reference for immunogenetic research, transplantation and disease-association studies in the Japanese population.