Identification of 11 novel HLA alleles found during typing of unrelated registry donors in China

HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action

BACKGROUND

HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR).

METHODS

For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used.

RESULTS

All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found.

CONCLUSIONS

Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.

HLA-C polymorphisms and PCR dropout in exons 2 and 3 of the Cw*0706 allele in sequence-based typing for unrelated Chinese marrow donors

To evaluate the accuracy of SBT protocols for HLA-C and to better understand the HLA-C polymorphism in Chinese, 1795 unrelated CMDP donors were typed at exons 2, 3, and 4 of the HLA-C gene using the Atria commercial kit. Of the study subjects, 1768 showed conclusive typing results, whereas the other 27 showed inconclusive results. Subsequent full-length cloning and haplotype sequencing showed that 11 of the 27 inconclusive results could be explained by the presence of nine novel alleles identified: Cw*0130, 0624, 070206, 075602, 0766, 0767, 0820, 0821, and 0827. These novel alleles were generated by a total of 10 coding-region substitutions, eight of them being located in the antigen-binding groove. Cw*0766 and Cw*075602 were detected three and two times, respectively, in the 1795 donors. The other 16 inconclusive samples were retested by SBT using our in-house PCR primers; all of them were found to carry Cw*0706, which dropped out in exons 2 and 3 in the initial PCR using the commercial primers amplifying from 5' UTR to intron 3. Our results showed the importance of the full-length genomic sequence and intronic SNPs for the development of more accurate SBT. The allele distribution and novel alleles detected in this study also provide further insights into the HLA-C polymorphism in the Chinese Han population.

Description of two novel alleles HLA-Cw*0766 and Cw*0767 identified in a Chinese Han individual by sequence-based typing

We report two novel HLA-C alleles, Cw*0766, and Cw*0767 identified in a Chinese voluntary stem cell donor. This sample was initially found by direct PCR-SBT with an inconclusive result. To clarify this unusual SBT result, the PCR product of HLA-C gene covering from exon 1-4 was subjected to cloning and haplotype sequencing and family study of HLA inheritance consisting of six members were confirmed. Novel Cw*0766 allele differs from the closest allele Cw*07020101 by single nucleotide change at genomic DNA nt 1651 C>A (codon 206 CTG>ATG) in exon 4, which results in an amino acid change Leu206Met. Another novel allele Cw*0767 differs from the closest allele Cw*07020103 by single nucleotide change at genomic DNA nt 930 A>T (codon 161 GAG>GTG) in exon 3, which results in an amino acid change Glu161Val. Family study demonstrated that the novel Cw*0766 allele segregating on an A*2402 B*4001 Cw*0766 DRB1*1202 haplotype was inherited from the mother of the propositus, whereas the novel Cw*0767 allele on haplotype A*1101 B*0702 Cw*0767 DRB1*0101 was inherited from the father.