Rare Copy Number Variants Increase Risk for Esotropia

Abstract

Purpose : Esotropia is the most common form of strabismus in European ancestry populations. Population, twin and family studies indicate a genetic predisposition, but no causative genes have been identified. Our recently published genome-wide association study (GWAS) identified a risk locus for non-accommodative esotropia in intron 1 of the WRB (tryptophan-rich basic protein) gene on chromosome 21. The risk SNP is differentially methylated and there is a skew toward paternal inheritance of the risk allele. Other neurological disorders, including Tourette syndrome, intellectual disability and autism, have recently been linked to DNA copy number variations (CNVs). We examined our cohort for rare CNVs, to determine if rare CNVs also contribute to esotropia.

Methods : Using the cohort of European ancestry esotropia patients included in the previous GWAS, we examined a subset of 1615 individuals with esotropia (both accommodative and non-accommodative) for CNVs and compared to 3922 publicly available controls. PennCNV and QuantiSNP were used to call CNVs from Illumina SNP chip data, for patients and controls. Only CNVs called by both programs, greater than 10kb and spanning 10 or more SNPs were included. Common CNVs and immunoglobulin regions, segmental duplications, centromeres and telomeres were excluded. Statistical comparisons were made using 1 million permutations in plink software. Significant CNVs were validated using digital droplet PCR (ddPCR).

Results : DNA duplications of regions of chromosomes 2, 4, 9, and 10 showed a significant association (p=1x10^-6) with esotropia. Each duplication was validated in esotropia patients by ddPCR. 127 of the 1615 esotropia patients had one or more of these four duplications. These duplications encompass 23 genes, non-coding RNAs or pseudogenes (3 on chr2, 1 on chr4, 9 on chr9, 10 on chr10).

Conclusions : This is the first study to report associations of esotropia with rare DNA CNVs. Esotropia is likely inherited as a complex trait, with multiple genetic variants contributing to risk. These duplications may alter gene dosages and/or disrupt genes or regulatory regions at their insertion sites. Future studies of the genes and regulatory regions involved and disrupted by the DNA duplications should provide insight into the pathophysiology of esotropia.

This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.