[Single nucleotide polymorphisms in 22 HLA-Cw alleles in Chinese Han population]

To analyze the molecular genetic polymorphism of full-length HLA-Cw gene, a total of 28 samples with known genotypes from Chinese Han population were amplified by long-range PCR using high-fidelity Pfu polymerase. A fragment 4.5 kb in length of HLA-Cw gene was subjected to cloning and haplotype sequencing. The single nucleotide polymorphisms (SNPs) in all segments of the whole region of HLA-Cw gene were analyzed. As a result, we detected 22 different HLA-Cw alleles in 28 samples, all of which were submitted to GenBank and the IMGT/HLA Database. Among the 22 HLA-Cw alleles, the intronic sequences of Cw*030301, Cw*0706 and Cw*140201 were firstly elucidated. The novel intronic sequence and the SNPs information may help to design allele-specific primers for accurate sequence-based typing (SBT) and to avoid allele dropout events in SBT test. We aligned all the diploid sequences using ClustalX program and imported them into Dnasp4.0 to calculate polymorphism in all coding- and non-coding regions. We found 244 SNPs and 10 insertion/deletions (Indels). According to the analysis of polymorphism level, phylogenetic trees and frequency spectrum, we proposed that the evolution of intron 4 and exon 5 was under balancing selection. Selection on these segments indicated that they may be functionally important in evolution of HLA-Cw gene. The full-length sequences obtained and related SNPs information can be used as resources of markers for high-resolution typing, complex diseases association studies and human evolution.