Analyses of low-frequency and rare variants associated with intraocular pressure

Abstract

Purpose : High intraocular pressure (IOP) is a major risk factor for primary open-angle glaucoma. Genome-wide association studies (GWAS) have successfully identified common variants associated with IOP. However, GWAS variants explain up to 1.2-1.5% of the variance leaving a substantial part of the genetic contribution unknown. To evaluate the association of rare and low-frequency exonic variants to IOP, we conducted a exome-sequencing and exome-array study in a family-based and population-based sample.

Methods : Discovery samples included 6296 individuals from the population-based Rotterdam study I (RS-I), and the family-based study Erasmus Rucphen Family (ERF). Among these, 2262 form RS-I and 1160 from ERF had exome-sequence data, and 1796 from RS-I and 1078 from ERF were genotyped in the Illumina HumanExome BeadChip. Association of rare and low-frequency variants (MAF<0.05) to IOP was tested using single variant analysis (SeqMeta), adjusting for age, sex and the first five principal components (RS-I) or family structure (ERF). Replication was sought in the TwinsUK cohort (n=1160, exomes), RS-I (independent set, n=1983), RS-II (n=2095) and RS-III (n=2992) imputed with the Haplotype Reference Consortium panel. Segregation of the rare variant in ERF pedigrees was studied and linkage was performed using Merlin.

Results : We identified six rare variants associated with IOP. Of these, one variant was significant in the combined replication analysis with a marginal P=0.03, the variant is located in CNKSR3, a gene implicated in sodium transport and aldosterone metabolism, as direct target of the aldosterone-activated mineralocorticoid receptor. In ERF we found an enrichment of the variant (MAF in ERF 0.01 vs 0.001 in RS). Pedigree analyses showed that the variant segregates in families with high IOP, explaining 26.8% of IOP heritability in these families (P=9.1x10^-03, LOD=1.47). RNA sequence data from 5 humans eyes showed that the gene is highly expressed in optic disc/nerve and retina, and less expressed in ciliary body and trabecular meshwork.

Conclusions : We identified a rare variant in the CNKSR3 gene which associates to IOP in the general population and segregates in families in ERF. Although CNKSR3 has been studied predominantly in the kidney our expression studies suggest that CNKSR3 may play a role in the local ocular renin-angiotensin system, a target in the IOP lowering treatment.

This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.