Unusual amplification pattern by SSP HLA-B typing led to discovery of a novel HLA-C allele

We report here the unique sequence of a novel human leucocyte antigen (HLA)-C allele resulted in amplification of a product with a primer pair used in sequence-specific primer (SSP) HLA-B typing, which led subsequently to identification of a new allele of Cw*0339 by sequence-based typing method. This new allele is closely related to Cw*031101 with only two nucleotide changes from T to G at position 97, and T to C at position 105 in the exon 2 region of HLA-C locus. The first nucleotide substitution causes an amino acid alteration from tyrosine to aspartic acid at amino acid residue 9 (Y to D), while the second one keeps alanine at residue 11 unchanged. Most interestingly, the nucleotide change from T to G at position 97 makes it identical to the 3' end sequence of one SSP of the commercial HLA-B SSP typing kit we were using. In this specific case, it resulted in amplification of a product of HLA-C gene instead of B gene.