Objective: To identify a novel human leukocyte antigen(HLA) allele in Chinese population.
Methods: HLA typing was carried out with polymerase chain reaction-sequence specific oligonucleotide probes (PCR-SSOP). The HLA-B exons 1-7 of the proband were amplified and the product was cloned using a TOPO TA cloning sequencing kit to separate the two alleles. Both strands of exons 2 and 3 of selected colonies were sequenced. Sequence-based typing (SBT) was used to identify and analyze the difference between the new allele and the closest matching HLA-B allele.
Results: HLA typing indicated a SSOP pattern which did not match with known HLA-B alleles. The results of the sequencing suggested the HLA-B alleles of the proband as B*59:01 and a novel allele. The HLA-B exon 3 sequence of the novel allele was different from any known alleles. This allele differs from the closest matching B*54:06 allele by 6 nucleotides, which included nt486 (G to C), nt527 (A to T), nt538 (T to C), nt539 (G to T), nt559 (C to A) and nt560 (T to C) in exon 3, resulting in substitutions of three amino acids including Glu to Val at codon 152, Trp to Leu at codon 156 and Leu to Thr at codon 163.
Conclusion: A novel HLA-B allele has been identified and has been designated as HLA-B*54:09 by WHO Nomenclature Committee for Factors of the HLA System.