文章摘要
王红,赵凯平.中国北京汉族人群和日本东京人群ROR2基因单核苷酸多态性比较[J].中华流行病学杂志,2011,32(11):1162-1165
中国北京汉族人群和日本东京人群ROR2基因单核苷酸多态性比较
Comparison of minor allele frequency and haplotype frequencies for single nucleotide polymorphisms in receptor tyrosine kinase-like orphan receptor 2 gene using HapMap data from Han Chinese in Beijing (CHB) and Japanese in Tokyo (JPT)
收稿日期:2011-05-20  出版日期:2014-09-18
DOI:
中文关键词: 受体酪氨酸激酶样孤立受体2;单核苷酸多态性
英文关键词: Receptor tyrosine kinase-like orphan receptor 2;Single nucleotide polymorphism
基金项目:美国国立卫生研究院国家牙科与颅面研究院基金(R21-DE-013707,R01-DE-014581);Fogarty基金(D43-TW006176)
作者单位E-mail
王红 北京大学公共卫生学院流行病与卫生统计学系 100191 hwang2010@yahoo.com 
赵凯平 北京大学公共卫生学院流行病与卫生统计学系 100191  
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中文摘要:
      目的比较中国北京汉族人群(CHB)和日本东京人群(JPT)受体酪氨酸激酶样孤立受体2(ROR2)基因单核苷酸多态性(SNP)的异同。方法 收集国际人类基因组单体型图计划(HapMap)公布的CHB及JPT的ROR2基因SNP数据,利用Haploview和SPSS 13.0软件区分纯合与非纯合基因型SNP,以基因型测定率>80%、H-W平衡(P>0.01)、MAF>0.01且无性别差异(P>0.05)为标准,在非纯合基因型SNP中确定合格SNP;标签SNP根据r2≥0.8或对数优势比(LOD)≥3进行确定;并比较合 格SNP及标签SNP的MAF、单体域及单体型频率。结果 CHB和JPT的ROR2基因SNP在两人群中 名称相同且均为404个,其中纯合基因型SNP为101个。两人群共有257个名称相同的合格SNP,其中224个(87.2%) SNP在两人群中的微效等位基因亦相同。257个合格SNP在CHB和JPT中分别形成18和27个单体域,除2个为JPT独有外,其余单体域在两人群完全或部分重叠。两人 群中名称相同的标签SNP为50个,分别占CHB和JPT各自标签SNP的64.9%和70.4%。结论 通过分析HapMap数据可避免将纯合基因型SNP纳入遗传易感性研究,CHB和JPT的ROR2基因SNP及单体域特征以共性为主,与人群的地域和种族属性一致。
英文摘要:
      Objective Single nucleotide polymorphisms(SNPs) in receptor tyrosine kinase like orphan receptor 2 (ROR2) gene were analyzed and compared between Han Chinese in Beijing(CHB) and Japanese in Tokyo(JPT) using the HapMap data,to provide basis for SNP determination.ROR2 gene related etiologic studies were conducted in the above mentioned two populations.Methods Monotonic and un-monotonic SNPs of ROR2 gene were distinguished by Haploview program.Minor allele frequency (MAF),haplotype blocks and haplotype frequencies were analyzed in eligible SNPs and tag SNPs respectively with genotyping call rate>80%,MAF>1%,H-Wequilibrium (P>0.01) and no gender difference (P>0.05).Tag SNPs were determined under thecriteria of r2≥0.8 or logarithm of the odd score (LOD)≥3 for pairwise eligible SNPs in CHB and JPT.Common tag SNPs for CHB and JPT were directly reported by Haploview program or being identified from those which were higly related to tag SNPs reported by haploview program under SPSS 13.0 software.Results A total of 404 common SNPs were provided for both CHB and JPT samples by HapMap,where 101 common monotonic SNPs between CHB and JPT had the common minor alleles.The common SNPs between CHB and JPT were 257.In the 257 common eligible SNPs,224 (87.2%) had common minor alleles.Among the 18 and 27 haplotype blocks identified in 257common eligible SNPs between CHB and JPT,except for 2 independent haplotype blocks identified only in JPT.Other haplotype blocks between CHB and JPT were overlapped partly or completely.A number of 50 common tag SNPs between CHB and JPT were determined and the proportions in CHB and JPT were 64.9% and 70.4% respectively.Conclusion Analysis of HapMap data provided an opportunity toavoid monotonic SNPsthathadbeenincluded inROR2generelated etiologic studies.SNPs inROR2genehadcommon features inalleles,MAF,haplotype blocks andhaplotype frequencies between CHB and JPT populations, which were consistent with the geographic and ethnic origins of the two populations.
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