Characterization of a novel DQB1 allele associated with HLA-DQw3: implications for oligotyping.

During HLA-DQ oligotyping, the presence of a novel HLA-DQB1 allele was suggested by a pattern of probe hybridization that was inconsistent with the presence of any possible combination of two known alleles. The nucleotide sequence of the second exon of the HLA-DQB1 gene was determined, revealing a novel HLA-DQB1 sequence differing from the DQB1*0301 allele by a single nucleotide substitution at codon 57. All published HLA-DQ oligotyping systems could assign inaccurate oligotypes when this allele is present. An additional amplification primer was utilized to achieve discrimination of all possible combinations of known HLA-DQB1 alleles.