Establishing the linkage disequilibrium pattern for the all-trans-retinol dehydrogenase (RDH8) gene

Objective: As part of an on-going effort to map genes involved in complex eye diseases, myopia in particular, single nucleotide polymorphisms (SNPs) and linkage disequilibrium (LD) pattern were used to identified the gene within and around the All-trans-retinol dehydrogenase (RDH8). Methods: Denaturing high-performance liquid chromatography (DHPLC) was used to screen SNPs in 4 DNA pools each consisting of DNA from five individuals, and genotypes identified SNPs coupled with DNA pooling strategy were performed in 150 Chinese subjects from Hong Kong. The identified common SNPs were included in LD and haplotype analysis using the Haploview2.05 and EH programs. Results: Fifteen SNPs were identified: 7 were common with the minor allele frequency > 0.05, and 10 were novel. Four SNPs in the 3′ region exhibited significant LD ( D′ > 0.75 and its confidence interval suggesting strong LD, r2 > 0.33, P < 0.031) and formed a haplotype block while 3 common SNPs in the 5′ region did not exhibit obvious LD. Conclusion: The block-like LD pattern existed around the RDH8 gene region suggest that one SNP (RDH8E5a probably) in the 3′ region and at least 2 SNPs in the 5′ region (RDH851 particularly) were needen in association studies involving RDH8.