PAX6 haplotypes are associated with high myopia in Han chinese

Abstract

Background: The paired box 6 (PAX6) gene is considered as a master gene for eye development. Linkage of myopia to the PAX6 region on chromosome 11p13 was shown in several studies, but the results for association between myopia and PAX6 were inconsistent so far.

Methodology/principal findings: We genotyped 16 single nucleotide polymorphisms (SNPs) in the PAX6 gene and its regulatory regions in an initial study for 300 high myopia cases and 300 controls (Group 1), and successfully replicated the positive results with another independent group of 299 high myopia cases and 299 controls (Group 2). Five SNPs were genotyped in the replication study. The spherical equivalent of subjects with high myopia was ≤-8.0 dioptres. The PLINK package was used for genetic data analysis. No association was found between each of the SNPs and high myopia. However, exhaustive sliding-window haplotype analysis highlighted an important role for rs12421026 because haplotypes containing this SNP were found to be associated with high myopia. The most significant results were given by the 4-SNP haplotype window consisting of rs2071754, rs3026393, rs1506 and rs12421026 (P = 3.54×10(-10), 4.06×10(-11) and 1.56×10(-18) for Group 1, Group 2 and Combined Group, respectively) and the 3-SNP haplotype window composed of rs3026393, rs1506 and rs12421026 (P = 5.48×10(-10), 7.93×10(-12) and 6.28×10(-23) for the three respective groups). The results remained significant after correction for multiple comparisons by permutations. The associated haplotyes found in a previous study were also successfully replicated in this study.

Conclusions/significance: PAX6 haplotypes are associated with susceptibility to the development of high myopia in Chinese. The PAX6 locus plays a role in high myopia.

Figure 1. Distribution of 16 single nucleotide polymorphisms (SNPs) in the PAX6 region.

The PAX6 region under study spans a genomic region of 324.6 kb (chr11: 31,484,873..31,809,434) together with different interesting features. Please refer to Table 1 for the rs numbers of the SNPs. (A) The top panel shows the physical positions (+ strand) of the 16 SNPs (S1 to S16, right to left) in the region under study, followed by positions of the SNPs genotyped by the HapMap project, the Entrez genes (ELP4 and PAX6) and the linkage disequilibrium (LD) pattern (r²) for HapMap Han Chinese. Note the low LD region in the 3′ end of the PAX6 gene. (Source: http://hapmap.ncbi.nlm.nih.gov/index.html.en) (B) A closer view of the 10-kb region in the 3′ end of the PAX6 gene, the binding sites for ten micro-RNAs as predicted by the programme TargetScan, and the sequence conservation across 28 mammalian species. (Source: http://genome.ucsc.edu/cgi-bin/hgGateway).

Figure 2. Linkage disequilibrium (LD) pattern across the 16 single nucleotide polymorphisms under study.

LD measures are expressed as r² in Group 1 subjects (cases and controls combined). The LD blocks are defined using the solid spine of LD algorithm of Haploview.