Frequency of Multigenic Variants Among Genes Regulating Retinal Vascular Development in FEVR Patients.

Abstract

Purpose : The potential contribution of multigenic variants in persons with Familial Exudative Vitreo Retinopathy (FEVR) remains as one possible factor contributing to the variable phenotypic severity seen even within a family. Understanding the frequency of combinations of protein-altering variants in different FEVR-related genes is an important first step to establishing if multigenic contributions require attention or can be disregarded. To determine the abundance of multigenic protein-altering variants, we employed a novel custom sequencing panel to analyze seven FEVR-related genes in FEVR patient samples.

Methods : Research genetic sequencing of samples from the Associated Retinal Consultants DNA Eye-Bank was approved by the Oakland University IRB. An Ampliseq panel was designed using the Illumina Design Studio. A three-pool PCR option was designed for a final 180 amplicons, 8 genes, 83 exons with 25 bp adjacent intron sequence. Seven FEVR genes and the Retinoschisis gene were included.: NDP (ChrX), CTNNB1 (Chr3); TSPAN12 (Chr7); KIF11 (Chr10), FZD4 (Chr11), LRP5 (Chr11), ZNF408 (Chr11), RS1(ChrX). A cohort of 76 samples comprised FEVR patients and some unaffected relatives. Ampliseq libraries from up to 50 samples were pooled per sequencing run using the Illumin iSeq-100 platform. Variant impacts and allele frequency data were determined from ClinVar and The Genome Aggregation Databases (gnomAD).

Results : 33 protein-altering variants were found with the following distribution: LRP5 13/33 (40%), FZD4 9/33 (27%), ZNF408 6/33 (18%), (KIF11 3/33 (9%), NDP 1/33 (3%), CTNNB1 1/33 (3%). 37% of persons sequenced had di-genic or tri-genic variants that alter protein sequences. The average number of genes with protein-altering variants was greater in samples from confirmed FEVR (1.46, N=30) compared to unaffected persons (0.95, N=20), (p=0.009).

Conclusions : Multigenic protein-altering variants were present in a substantial fraction of FEVR subjects, 37%. While the contributions to disease are unknown for most of the variants in a multigenic context, their greater multigenic frequency in FEVR subjects suggests that potential multiple endothelial gene contributions to variable phenotypes are a possibility that clinics should consider for patients with FEVR / Norrie Disease.

This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.

 

Gene count occurrences of protein-altering variants in a group of FEVR subjects versus unaffected subjects in this study.