Wang Hong, Zhao Kai-ping
Department of Epidemiology and Biostatistics, Peking University, Beijing, China.
Zhonghua Liu Xing Bing Xue Za Zhi. 2011 Nov;32(11):1162-5.
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.
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-W equilibrium (P > 0.01) and no gender difference (P > 0.05). Tag SNPs were determined under the criteria of r(2) ≥ 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.
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 257 common 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.
Analysis of HapMap data provided an opportunity to avoid monotonic SNPs that had been included in ROR2 gene related etiologic studies. SNPs in ROR2 gene had common features in alleles, MAF, haplotype blocks and haplotype frequencies between CHB and JPT populations, which were consistent with the geographic and ethnic origins of the two populations.
利用HapMap数据对北京汉族（CHB）和东京日本人（JPT）的受体酪氨酸激酶样孤儿受体2（ROR2）基因中的单核苷酸多态性（SNP）进行分析和比较，为SNP的确定提供依据。在上述两个人群中开展ROR2基因相关病因学研究。
通过Haploview程序区分ROR2基因的单调和非单调SNP。对基因分型检出率>80%、小等位基因频率（MAF）>1%、哈迪-温伯格平衡（P>0.01）且无性别差异（P>0.05）的合格SNP和标签SNP分别分析MAF、单倍型块和单倍型频率。在CHB和JPT中，成对合格SNP根据r(2)≥0.8或对数优势分数（LOD）≥3的标准确定标签SNP。CHB和JPT的常见标签SNP由Haploview程序直接报告，或在SPSS 13.0软件下从与Haploview程序报告的标签SNP高度相关的SNP中识别。
HapMap为CHB和JPT样本共提供404个常见SNP，其中CHB和JPT之间有101个常见的单调SNP具有共同的小等位基因。CHB和JPT之间的常见SNP有257个。在这257个合格的常见SNP中，224个（87.2%）具有共同的小等位基因。在CHB和JPT之间257个合格的常见SNP中确定的18个和27个单倍型块中，除了仅在JPT中确定的2个独立单倍型块外，CHB和JPT之间的其他单倍型块部分或完全重叠。确定了CHB和JPT之间的50个常见标签SNP，在CHB和JPT中的比例分别为64.9%和70.4%。
HapMap数据分析为避免ROR2基因相关病因学研究中已包含的单调SNP提供了机会。ROR2基因中的SNP在CHB和JPT人群的等位基因、MAF、单倍型块和单倍型频率方面具有共同特征，这与两个人群的地理和种族起源一致。
