Diversity and Frequency of HLA-DRB1*15:03-DRB5 Haplotypes in a Large Cohort: The Case of the Absent HLA-DRB5 Revisited

Abstract

The HLA class II region contains nine DRB genes: DRB1, DRB3, DRB4 and DRB5 express functional gene products, whereas DRB2, DRB6, DRB7, DRB8 and DRB9 are pseudogenes. In this study, we assessed the frequency and diversity of two functional genes, DRB1 and DRB5; in particular, HLA-DRB1*15:03 with absence of the associated HLA-DRB5*01:01 allele (DRB1*15:03 positive DRB5*01:01 negative). We aimed to determine the frequency of DRB1*15:03 positive DRB5*01:01 negative in this cohort and to define any putative full or partial haplotypes that may show this genotype pattern. We performed HLA typing by NGS using One Lambda AllType or CareDx AlloSeq Tx17 on 6268 solid organ transplant (SOT) samples using DNA extracted from either buccal swabs or whole blood. The absence of HLA-DRB5 was confirmed by One Lambda LABType rSSOP. Confirmation of DRB1*15 homozygotes was performed by CareDx Copy Number (RUO) tool. In the present cohort, 554 (8.8%) individuals were identified as HLA-DRB1*15:03 positive. Of those, 48 individuals (8.7% of HLA-DRB1*15:03 positive) did not have the associated DRB5*01:01 allele present. We believe that this percentage could be as high as 11.2% when considering DRB1*15:XX homozygotes. Although linkage disequilibrium analysis showed strong LD between DRB1*15:03 and DRB5*01:01 (D′ = 0.89), supporting their co-inheritance on the same haplotype block, a moderate correlation coefficient (r² = 0.302) implied that DRB5*01:01 is not always present in all DRB1*15:03 carriers. Extended haplotypes associated with this phenomenon were constructed and characterised. Certain HLA-A, B, DRB1 haplotypes were strongly predictive of absent DRB5. To our knowledge, this is the largest cohort ascertaining the diversity and frequency of the HLA-DRB1*15:03 apparent haplotypes. Our results show a considerable proportion of DRB1*15:03 positive individuals lack the DRB5 gene. The results of this study are useful for unrelated donor research, transplantation, anthropological and disease association studies.