Whole Exome sequencing to identify the pharmacogenetic basis of retinal fluid clearance in anti-VEGF treated AMD

Abstract

Purpose : Intravitreal injection of anti-vascular endothelial growth factor (anti-VEGF) is the predominant mode of treatment for the neovascular form of Age-related macular degeneration (nAMD). However, treatment response can vary and may be due to genetic variation. We wished to identify genetic variants that might be involved in resolution of retinal fluid following anti-VEGF treatment in nAMD patients by undertaking whole exome sequencing (WES).

Methods : A total of 54 treatment naïve nAMD patients were recruited from the Royal Victorian Eye and Ear Hospital, Melbourne. Optical Coherence Tomography (OCT) was obtained at both the first and the 4^th review visit. The primary treatment outcome indicator was qualitative OCT fluid persistence (non-responders, n=29) and resolution of all fluid (responder, n=25) after 3 injections with anti-VEGF compared to baseline OCT fluid. WES was performed using an Illumina HiSeq 2000 platform followed by an in-house downstream analysis pipeline (Genome Institute of Singapore). Logistic regression was performed to determine genetic associations with fluid presence using plink software. Associated genetic variants from the discovery phase were replicated in an independent anti-VEGF treated nAMD cohort (responders =121, non-responders =39). Meta-analysis on both cohorts was performed using METAL and gene enrichment using Gene Ontology enRIchment anaLysis and visuaLizAtion tool (GORILLA).

Results :
In the discovery phase, 53% of patients had retinal fluid after 3 anti-VEGF injections. WES identified a total of 123,192 variants passing quality filters with a minor allele frequency threshold (MAF ≦0.01). Four variants showed suggestive association (P < 8x10⁻⁴) with fluid presence in discovery, and the meta-analysis of both cohorts (n=215) identified the top SNP as a missense variant in an olfactory gene on chromosome 14 (P=3.5x10⁻³). All 79,620 coding variants were mapped to 13,224 genes and enrichment analysis revealed a G-protein coupled receptor (GPCR) pathway (corrected P=8x10⁻¹⁵) suggesting the involvement of cell signaling molecules in anti-VEGF treatment response in nAMD patients.

Conclusions : WES identified gene variants associated with the anatomical feature of retinal fluid presence/ absence in an olfactory gene indicating a GPCR pathway influences anti-VEGF treatment response.

This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.