DRB3 alleles with variations in the annealing sites of commonly used amplification primers

New HLA alleles are often identified initially from observing uncommon patterns found in low‐resolution typing performed via polymerase chain reaction using sequence‐specific oligonucleotide probes (PCR‐SSOP). Recently, the HLA‐DR oligotyping analysis of two Caucasian, one Caucasian/American Indian and two African American individuals resulted in the identification of three novel DRB3 alleles. Using DRB‐specific primer sets commonly employed in amplification‐based typing, all four individuals were originally characterized as DRB3 negative. Direct sequencing identified DRB3*0104 (variation at codon 8, T CG instead of T TG), and DRB3*0101202 (variation at intron (−13), G instead of C). One individual appeared to carry a DR52‐associated DRB1 allele without an associated DRB3 allele. Lack of conservation at the junction of intron 1 and exon 2 of the DRB3 gene suggests that commonly used DRB‐specific primer sets may need to be modified.