汉族人群中22个HLA-Cw等位基因全长序列单核苷酸多态性分析

doi:10.3724/SP.J.1005.2010.00473

遗传 ›› 2010, Vol. 32 ›› Issue (5): 473-497.doi: 10.3724/SP.J.1005.2010.00473

汉族人群中22个HLA-Cw等位基因全长序列单核苷酸多态性分析

曾健强, 徐筠娉, 王大明, 高素青, 邹红岩, 邓志辉

深圳市血液中心, 深圳市组织配型与免疫遗传重点实验室, 深圳 518035

收稿日期:2009-10-13 修回日期:2010-01-06 出版日期:2010-05-20 发布日期:2010-05-05
通讯作者: 徐筠娉 E-mail:yunpingxu1982@yahoo.com.cn
基金资助:
深圳市科技计划项目(编号：200802116), 广东省科技计划项目(编号：2008B030301277)和广东省自然科学基金项目 (编号：9451803501004124)资助

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

ZENG Jian-Qiang, XU Yun-Ping, WANG Da-Ming, GAO Su-Qing, ZOU Hong-Yan,DENG Zhi-Hui

Shenzhen Key Laboratory of Histocompatibility and Immunogenetics, Shenzhen Blood Center, Shenzhen 518035, China

Received:2009-10-13 Revised:2010-01-06 Online:2010-05-20 Published:2010-05-05
Contact: XU Yun-Ping E-mail:yunpingxu1982@yahoo.com.cn

摘要/Abstract

摘要：

为探讨HLA-Cw (Human leukocyte antigen-Cw)基因全长序列分子遗传多态性, 文章对28个HLA-Cw基因型已知的汉族个体样本, 采用长距离PCR技术和高保真性的Pfu酶, 扩增HLA-Cw基因全长序列4.5 kb, 进行分子克隆和单倍体测序。采用群体遗传学研究方法分析了HLA-Cw等位基因全长序列中各亚区的单核苷酸多态性。结果表明: 在28个样本中共检测出22种等位基因, 序列均已提交GenBank和国际IMGT/HLA数据库并获得了认可; 其中Cw*0706、Cw*030301、Cw*140201的全长序列为首次报道, 尤其是Cw*0706内含子序列的获得, 能够重新设计对该等位基因测序分型的引物, 避免测序分型中可能对这一等位基因的漏检。将28个样本的56条单倍体序列用Clustal软件进行序列排比, 输入到DnaSP4.0进行多态性分析, 共发现244个SNPs, 10处插入/缺失多态性。对HLA-Cw等位基因各亚区多态性的分析, 发现第4内含子及以前并没有受到关注的第5外显子受到平衡选择的作用, 在进化中受到了选择压力, 预示着它们在免疫系统的进化过程中可能扮演着重要的角色。

关键词: 人类白细胞抗原, HLA-Cw基因, 基因组全长序列, 克隆和测序分析, 单核苷酸多态性

Abstract:

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.

Key words: human leukocyte antigen (HLA), HLA-Cw gene, genomic full length, cloning and sequencing analysis, single nucleotide polymorphisms (SNPs)

曾健强，徐筠娉，王大明，高素青，邹红岩，邓志辉. 汉族人群中22个HLA-Cw等位基因全长序列单核苷酸多态性分析[J]. 遗传, 2010, 32(5): 473-497.

CENG Jian-Jiang, XU Jun-Pin, WANG Da-Meng, GAO Su-Jing, JU Gong-Yan, DENG Zhi-Hui. Single nucleotide polymorphisms in 22 HLA-Cw alleles in Chinese Han population[J]. HEREDITAS, 2010, 32(5): 473-497.

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汉族人群中22个HLA-Cw等位基因全长序列单核苷酸多态性分析

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

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