Strategy for distinguishing a new DQB 1 allele (DQB1(*)0611) from the closely related DQB 1(*)0602 allele via sequence specific PCR or direct DNA sequencing

A novel DQ6 allele (DQB 1(*)0611) was identified via direct DNA sequencing in an African-American donor for bone marrow transplantation. The allele was not suspected on the basis of a sequence specific PCR assay which instead indicated the presence of DQB1(*)0602. DQB1(*)0602 and DQB1(*)0611 differ in exon 2 only at codon 9 resulting in a tyrosine substitution for phenylalanine. A modification of current DQB 1 sequence specific PCR assays was devised which allows distinction between the closely related DQB1(*)0602 and DQB1(*)0611 alleles. Preliminary allele frequency studies suggest that DQB1(*)0611 is rare both in a non-African American sample and in Americans of African descent carrying DR11, DQ6 haplotypes. The selection of various DQB1(*)0611 detection methods is discussed.