PMID: 22336557Feb 18, 2012Paper

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)

Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi
Hong Wang, Kai-ping Zhao

Abstract

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...Continue Reading

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