[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)].

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-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.

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 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.

CONCLUSION

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.