[Comparison of minor allele frequencies and haplotype frequencies for single nucleotide polymorphisms in ROR2 gene using HapMap data for Chinese Hans in Beijing and Yoruban in Ibadan in Nigeria].

OBJECTIVE

To provide basis for single nucleotide polymorphisms (SNPs) determination and analysis for ROR2 genes related etiologic studies in Chinese Hans in Beijing (CHB) and Yoruban in Ibadan in Nigeria (YRI) populations.

METHODS

SNPs in ROR2 gene were analyzed and compared for minor allele frequencies (MAFs), haplotype frequencies, linkage disequilibrium patterns, and tag SNPs using CHB and YRI data from HapMap by Haploview 4.2 program. SNPs were screened for eligibility using quality control criteria of genotyping call rate>80%, Hardy-Weinberg equilibrium test P>0.01, gender difference P>0.05 and MAF>0.01. Tag SNPs were determined under the criteria for r(2)≥0.8 and logarithm of the odds radio≥3 in pairwise eligible SNPs and compared between the CHB and YRI samples. Common Tag SNPs for CHB and YRI were reported by Haploview program directly or identified among SNPs which were higly related to Haploview program directly reported tag SNPs by SPSS 13.0.

RESULTS

Among the 404 and 403 SNPs genotyped in ROR2 genes in the CHB and YRI samples released by HapMap project, there were five SNPs located at exon 6 or 9 where changes of alleles for rs1076112 and rs10820900 caused missense mutation. Among the 394 SNPs genotyped in both the populations, a total number of 101 (25.6%) SNPs were monotonic among which 66 (65.3%) SNPs were common in both CHB and YRI. The rs1135150 and rs2230577 which were monotonic in YRI and eligible in CHB located at exon 9. Nine ungenotyped SNPs in CHB were all eligible in YRI, and 6 out of 10 ungenotyped SNPs in YRI were eligible in CHB. The proportion of common SNPs (214) were 81.4% and 73.3% in eligible CHB (263) and YRI (292) SNPs where 177 (82.7%) had the same minor alleles and 30 SNPs also had MAF difference ratios<20% that represented 11.4% and 10.3% of the total number of eligible SNPs in CHB and YRI respectively. Among the 18 and 26 haplotype blocks formed in 214 common eligible SNPs, two independent haplotype blocks were unique in CHB, one was unique in YRI, one was common between CHB and YRI, and the remaining 15 haplotype blocks in CHB were partially overlapped with the additional 24 ones formed in the YRI samples. A number of 44 common tag SNPs were determined in 77 (57.1%) CHB and 69 (35.2%) YRI tag SNPs where 35 were identified by Haploview program directly and 9 among highly related SNPs of tag SNPs by SPSS 13.0. Two unique haplotype blocks were formed in 44 common tag SNPs in CHB and YRI, respectivey. The cumulative haplotype frequencies were 91.8% and 93.9% for the top three haplotypes for each haplotype block in CHB and the numbers for the top two haplotypes were 81.4% and 92.5% for each haplotype block in YRI.

CONCLUSION

Proportion of monotonic SNPs in ROR2 genes was rather big in the CHB and YRI samples tested by HapMap. SNPs in ROR2 genes mainly showed unique features in terms of minor alleles, MAF, haplotype blocks and haplotype frequencies for CHB and YRI populatons, which is consistent with their racial groups.