OR25. The highly polymorphic HLA-DRA Gene: conserved and diverse regions within the HLA-DRA gene imply haplotypes of DRA[formula omitted]DRB3/4/5[formula omitted]DRB1[formula omitted]DQB1

Abstract

Aim HLA-DRA is highly conserved compared to the other HLA genes. The gene is represented in IPD-IMGT/HLA by 7 alleles encoding two distinct proteins, and we observed that the known DRA alleles have two deletions in intron 4, forming 3 characteristic patterns. We are interested in elucidating the polymorphism of DRA in relation to DR-DQ haplotypes using full-length genomic sequencing. Methods Our laboratory performed full-length DRA sequencing on 70 samples, using MinION and confirming novel SNPs with Sanger SBT. Full-length reads were aligned against reference sequences from IPD-IMGT/HLA to identify sequence polymorphisms and deletion patterns. These polymorphisms were analyzed in the context of HLA-DRB1, -DRB3,4,5, and -DQB1 alleles. Results HLA-DRA alleles represented in IPD-IMGT/HLA are a underestimation of the diversity in the sequence polymorphism. More than 40 novel DRA alleles were identified based on intronic polymorphisms, but exon 2 remains remarkably conserved. Polymorphisms in exons 3 and 4 were confirmed, but no new exonic polymorphism was identified. 19 previously unrepresented SNP positions were identified within the 5711bp region represented in IPD-IMGT/HLA, and the remaining SNPs are combinations of the 61 known polymorphisms. HLA-DRB1 alleles were correlated with the observed intronic deletion patterns. Specifically, DRA alleles corresponding to DRB1∗04, DRB1∗07, and DRB1∗11 groups are correlated with one deletion pattern. DRA deletion patterns that are linked with the DRB1∗03 and DRB1∗13 were correlated with specific DRB3 and DQB1 alleles. Similarly, DRA deletion patterns correlated with DRB1∗15 alleles were also correlated with DRB5 and DQB1. Conclusions HLA-DRA is highly polymorphic, but has conserved exons, suggesting the gene plays a crucial role in immune responses. The observed polymorphism patterns suggest the existence of recombination site(s) within DRA, and the intron deletions give clues about the DRA ∼ DRB3/4/5 ∼ DRB1 ∼ DQB1 haplotypes. Patterns in polymorphisms may represent different evolutionary lineages, suggesting different origins of the DRA genes in the ancestral haplotypes. Extending the samples for further analysis by computational haplotyping will elucidate the origin of the DRA genes in this haplotype.