P047 Analysis of 25,000 Caucasian samples reveals tight linkage between SNP rs9277534 and high resolution typing of HLA-DPB1

Abstract

Aim HLA-DPB1 mismatching between the patient and unrelated donor is known to increase the risk of acute graft-versus-host-disease (GvHD) after hematopoietic stem cell transplantation. If only HLA- DPB1 mismatched donors are available, the genotype defined by the Single Nucleotide Polymorphism (SNP) rs9277534 can be used to select mismatched donors that are well-tolerated. However, since rs9277534 resides within the 3′ untranslated region (UTR), it usually is not analyzed during DPB1 routine typing. To verify whether rs9277534 can be inferred from standard DPB1-typing, we analyzed over 25,000 samples of mostly Caucasian origin for linkage between rs9277534 and high resolution HLA-DPB1 typing results based on sequencing exons 2 and 3. Methods rs9277534 located in the 3′ UTR was amplified by PCR and sequenced on Illumina MiSeq or Hiseq instruments. SNP calling was performed with FasType (DKMS Life Science Lab). DPB1 typing based on sequencing exons 2 and 3 was performed as described before. Results 99.5% of the samples carried the expected rs9277534 allele based on typing of exons 2 and 3. Only in one sample (0.004%), the expected linkage between exon 2 and rs9277534 was broken. In the remaining 0.5% samples, the linkage could not be established because of remaining ambiguities due to missing phasing between exons 2 and 3. Phasing a subset of these samples with PacBio whole gene DPB1 sequencing confirmed the presence of alleles with the expected linkage to the identified rs9277534 variants. Further, we have established the rs9277534 linkage for 23 DPB1 alleles for which the 3′ UTR sequence is so far unknown within IMGT. Conclusions HLA-DPB1 typing of exons 2 and 3 is sufficient to infer rs9277534, a marker for DPB1 expression. This information could be used to select HLA-DPB1-mismatched donors that do not increase the risk of GvHD. E.W. Petersdorf: Grant/Research Support; Company/Organization; National Institutes of Health. Employee; Company/Organization; Frederick National Laboratory for Cancer Research, National Institutes of Health.