Abstract
All-trans-retinol dehydrogenase (RDH8) is a visual cycle enzyme that reduces all-trans-retinal to all-trans-retinol. As part of an on-going effort to map genes involved in complex eye diseases, myopia in particular, using association studies, single nucleotide polymorphisms (SNPs) were identified and linkage disequilibrium (LD) pattern was established within and around the RDH8 gene. We used denaturing high-performance liquid chromatography (DHPLC) to screen SNPs in four DNA pools each consisting of DNA from five individuals and genotyped the identified SNPs in 150 Chinese subjects from Hong Kong. Fifteen SNPs were identified: seven were common with the minor allele frequency >0.05 and ten were novel. Common SNPs were included in LD and haplotype analysis using the ASSOCIATE and EH programmes. Four SNPs in the 3’ region exhibited significant LD and formed a haplotype block, while three common SNPs in the 5’ region did not exhibit useful LD. The LD pattern around the RDH8 gene suggested that one SNP from the 3’region and two to three SNPs from the 5’ region were needed in association studies involving RDH8. Our results demonstrated the efficiency of DHPLC in screening SNPs when coupled with DNA pooling strategy and in genotyping SNPs.
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Acknowledgements
The SNP project for myopia candidate genes was supported by an Internal Competitive Research Grant (A-PC13), The Hong Kong Polytechnic University (PolyU). Wei Han was supported by a PolyU competitive grant (G-T538) for Joint Supervision of Ph.D. students with Zhejiang University. The Wave DNA Fragment Analysis System was purchased with a PolyU Big Equipment Grant (G.53.27.9027), and Genetic Analyzer 310 with funds from three sources: a departmental fund (School of Nursing, PolyU); Faculty Dean’s Reserve (1.53.27.8721; Faculty of Health and Social Sciences, PolyU); and an Area for Strategic Development Fund for Myopia Research (A362, Department of Optometry and Radiography, PolyU).
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Han, W., Yip, S.P., Wang, J. et al. Using denaturing HPLC for SNP discovery and genotyping, and establishing the linkage disequilibrium pattern for the all-trans-retinol dehydrogenase (RDH8) gene. J Hum Genet 49, 16–23 (2004). https://doi.org/10.1007/s10038-003-0100-9
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DOI: https://doi.org/10.1007/s10038-003-0100-9
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