An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: Analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome Iq2I-q25
An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: Analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome Iq2I-q25
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DOI：
10.1186/1471-2156-9-19
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发表时间：
2008-02-27
期刊：
影响因子：
2.9
通讯作者：
Xiang, Kunsan
中科院分区：
文献类型：
--
作者：
Hu, Cheng;Jia, Weiping;Xiang, Kunsan
背景资料：人类基因组单核苷酸多态性（SNPs）是人类基因组中的一个重要组成部分，人类基因组单核苷酸多态性（SNPs）是人类基因组中最常见的单核苷酸多态性。为了检验北京汉族人HapMap数据对上海南方汉族人的可转移性，我们对80名无关的上海人和45名中国人HapMap数据中染色体Iq 2 I-q25上21 Mb区域的4,500多个SNP的基因型进行了比较分析。结果：在去除质量控制失败的SNP和不在HapMap面板中的SNP后，分析了3042个SNP。比较了HapMap群体和上海地区中国人群的等位基因频率分布、连锁不平衡模式、单倍型频率分布和标记SNP的可传递性。在4个HapMap群体中，北京人与上海人在等位基因频率、连锁不平衡和单倍型频率上的相关性最好。在上海样本中，以不同阈值对从4个HapMap群体中选择的标记SNP集进行评估。在r（2）= 0.8或0.5的阈值下，中国人和日本人的HapMap数据的覆盖率和标记效率均高于高加索人和非洲人。结论：我们的研究支持HapMap北京中国人SNP数据在中国南方人群复杂疾病研究中的适用性。
Background: The HapMap project aimed to catalog millions of common single nucleotide polymorphisms ( SNPs) in the human genome in four major populations, in order to facilitate association studies of complex diseases. To examine the transferability of Han Chinese in Beijing HapMap data to the Southern Han Chinese in Shanghai, we performed comparative analyses between genotypes from over 4,500 SNPs in a 21 Mb region on chromosome Iq2I-q25 in 80 unrelated Shanghai Chinese and 45 HapMap Chinese data. Results: Three thousand and forty-two SNPs were analyzed after removal of SNPs that failed quality control and those not in the HapMap panel. We compared the allele frequency distributions, linkage disequilibrium patterns, haplotype frequency distributions and tagging SNP sets transferability between the HapMap population and Shanghai Chinese population. Among the four HapMap populations, Beijing Chinese showed the best correlation with Shanghai population on allele frequencies, linkage disequilibrium and haplotype frequencies. Tagging SNP sets selected from four HapMap populations at different thresholds were evaluated in the Shanghai sample. Under the threshold of r(2) equal to 0.8 or 0.5, both HapMap Chinese and Japanese data showed better coverage and tagging efficiency than Caucasian and African data. Conclusion: Our study supported the applicability of HapMap Beijing Chinese SNP data to the study of complex diseases among southern Chinese population.