OR33 Allelic diversity and haplotype structure of HLA-DPB1 based on full-length characterization of most CWD alleles

Abstract

Aim Currently, full-length sequences are known for only 12 out of 644 HLA-DPB1 alleles, covering 6 of 54 common and well-documented (CWD) alleles. To better understand the patterns and types of polymorphisms in the HLA-DPB1 gene, we full-length sequenced a set of donors from the DKMS Life Science Lab sample repository selected with the goal to represent all common and well-documented (CWD) alleles. Methods Primers were developed flanking the UTR-regions of DPB1 resulting in a 12 kb amplicon. After long range PCR two redundant sequencing strategies were employed: Shotgun sequencing on Illumina MiSeq instruments and Single Molecule Real Time (SMRT) sequencing on PacBio RS II instruments. Phase-defined consensus sequences were generated from PacBio data and confirmed with short reads using the DR2S software (DKMS Life Science Lab). Results We successfully sequenced the full-length sequences of 173 samples (346 haplotypes) covering 37 common, 14 well-documented, and 3 not-CWD-defined DPB1 alleles. An additional 84 allelic variants were found based on variation outside of exons 2 and 3. Nine previously known full-length DPB1 alleles were confirmed at least once. For these alleles 45 novel intron variants were found. Novel variation is present most densely within the 5 ′ UTR and introns 1 and 2. A phylogenetic analysis of the 138 unique DPB1 alleles shows the existence of two major evolutionary branches characterized by a 4 Kb block at the 3 ′ end which is composed of only two haplogroups with no evidence of historical recombination. Conclusion Here we present full-length sequences of 138 unique DPB1 alleles covering most common and all well-documented (CWD) alleles. We observe distinct differences in recombination rates within DPB1 indicating differential evolutionary forces acting on different parts of the gene.