Genetic variants at 13q12.12 are associated with high myopia in the Han Chinese population

Abstract

High myopia, which is extremely prevalent in the Chinese population, is one of the leading causes of blindness in the world. Genetic factors play a critical role in the development of the condition. To identify the genetic variants associated with high myopia in the Han Chinese, we conducted a genome-wide association study (GWAS) of 493,947 SNPs in 1088 individuals (419 cases and 669 controls) from a Han Chinese cohort and followed up on signals that were associated with p < 1.0 × 10(-4) in three independent cohorts (combined, 2803 cases and 5642 controls). We identified a significant association between high myopia and a variant at 13q12.12 (rs9318086, combined p = 1.91 × 10(-16), heterozygous odds ratio = 1.32, and homozygous odds ratio = 1.64). Furthermore, five additional SNPs (rs9510902, rs3794338, rs1886970, rs7325450, and rs7331047) in the same linkage disequilibrium (LD) block with rs9318086 also proved to be significantly associated with high myopia in the Han Chinese population; p values ranged from 5.46 × 10(-11) to 6.16 × 10(-16). This associated locus contains three genes-MIPEP, C1QTNF9B-AS1, and C1QTNF9B. MIPEP and C1QTNF9B were found to be expressed in the retina and retinal pigment epithelium (RPE) and are more likely than C1QTNF9B-AS1 to be associated with high myopia given the evidence of retinal signaling that controls eye growth. Our results suggest that the variants at 13q12.12 are associated with high myopia.

Figure 1

Genome-Wide-Association Results from the Initial GWAS (A) Quantile-quantile plots of the observed p values (–log₁₀P) for association. (B) The genome-wide distribution of –log₁₀ p values from the unadjusted Cochran-Armitage trend test is shown across the chromosomes. Values that take into account genetic matching and correction for the inflation factor of 1.07 are shown for 493,947 SNPs that were of sufficient quality, after quality-control filtering, in 419 unrelated Han Chinese patients with high myopia and in 699 unrelated Han Chinese controls. Each chromosome is depicted in a different color. –log₁₀(UNADJ) refers to −log₁₀ p value of the Cochran-Armitage trend test unadjusted by multiple testing. The dotted line indicates the genome-wide threshold for further follow-up studies (p < 1.0 × 10⁻⁴).

Figure 2

The 13q12.12 Region and Its Association with High Myopia in Han Chinese (A) Results of the GWAS and replication identify 13q12.12 as a risk locus. Plot of –log₁₀ p values of 18 SNPs genotyped in the GWAS within a 200 kb region surrounding this locus at 13q12.12. The color of each SNP spot reflects its r² value: The top SNP (rs9318086) changes from red to white as the r² value decreases. Estimated recombination rates were adapted from the University of California at Santa Cruz Genome Browser. The small diamonds indicate the p values of the initial GWAS (upper panel). The lower panel shows the LD block of nine SNPs (p values less than 0.05 in our GWAS data) surrounding the 13q12.12 region. (B) The p values of rs9318086 and rs1886970 were 1.91 × 10⁻¹⁶ and 2.31 × 10⁻¹⁴, respectively, after all four datasets composed of 3222 cases and 6311 controls were combined (black circle). Four additional SNPs (rs9510902, rs3794338, rs7325450 and rs7331047) in the same LD block with rs9318086 and rs1886970 were shown to have a similar association with high myopia; p values ranged from 5.46 × 10⁻¹¹ to 8.68 × 10⁻¹⁶ after all four datasets composed of 3222 cases and 5642 controls were combined (669 controls from the GWAS were absent because no DNA was available at this stage) (red square). The linkage disequilibrium block structure was examined with the program Haploview (Vision 4.0). The D′ values and r² values for all pairs of SNPs were calculated, and the haplotype blocks were estimated with the program Haploview.

Figure 3

Expression Analysis with RT-PCR of MIPEP, C1QTNF9B, and C1QTNF9B-AS1 in Human Tissues and Cell Lines We examined the expression of these three genes in different human tissues (human blood, choroid, placenta, and retina) and human cell lines (retinal pigment epithelium cell line [D407], kidney cell line [HEK293], and ovarian cell line [A2870]) by using RT-PCR. GAPDH was used as an internal control for cDNA quantification.