Whole exome sequencing in advanced POAG cases of GWAS associated candidate genes identifies significant enrichment of rare variants in CARD10.

Abstract

Purpose : This study uses a subset of well characterised cases with POAG with advanced visual field loss and young age of onset from the Australian and New Zealand Registry of Advanced Glaucoma to determine whether rare delerious variants in GWAS associated genes for POAG and its endophenotypes IOP, optic disc morphology and CCT are significantly enriched in cases versus matched controls.

Methods : 65 genes of interest were selected which had been reported to be associated at the level of genome wide significance in GWAS studies with either POAG, or one of its endophenotypes IOP, optic disc morphology, or CCT. Whole exome sequencing (WES) was performed on 187 cases with advanced visual field loss comprising 122 high tension and 65 normal tension cases with POAG. Cases with mutations in myocilin were excluded. 103 non glaucoma cases were subjected to WES contemporaneously. A further 993 Australian controls were subsequently joint called with the discovery set. Filters were applied to limit sequence variants to rare (<1%), and predicted pathogenic in SIFT or polyphen. Genes showing significant enrichment were further evaluated in public domain controls using the ExAC database.

Results : Sixty-five GWAS associated glaucoma genes were analysed in this study. Rare pathogenic variants in the whole GWAS gene set were found more frequently in the cases versus controls, but this did not reach statistical significance (OR = 1.33, p = 0.069). Four genes (CARD10, CWC27, RERE and USP37) were enriched in the glaucoma cohort (p < 0.05). CARD10 survived Bonferroni correction (OR = 13.2, corrected p = 4.51×10^-3) with predicted pathogenic variants found in 8/187 (4.3%) of the POAG cohort.

Conclusions : Rare predicted deleterious variants in GWAS associated POAG associated genes such as CDKN2A/B, TMCO1, CAV1/2, and SIX5/6 were not found to be enriched in this study. Rare predicted deleterious variants in CARD10 are significantly enriched in POAG cases with advanced visual field loss versus controls. Common SNPs around CARD10 have been associated with optic disc area, and vertical cup to disc ratio. CARD10 is a key apoptosis regulator involved in NFKB signalling and cell cycle regulation. It is biologically plausible that loss of function of CARD10 could increase retinal ganglion cell susceptibility to apoptosis.

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