Pathogenic structural and non-coding variants in retinal dystrophy identified through the 100,000 genomes project

Abstract

Purpose : To characterise pathogenic variants in whole genome sequencing (WGS) data from a cohort of patients with inherited retinal disease (IRD).

Methods : Patients and families were recruited from the inherited retinal disease clinics at Moorfields Eye Hospital, London as part of the UK 100,000 genomes project. A cohort of 358 probands with a broad spectrum of IRD underwent WGS and bioinformatic analysis for pathogenic variants in a virtual panel of 313 genes associated with posterior segment abnormalities. Potential pathogenic structural and non-coding variants were selected for downstream functional analysis by applying an integrated analysis pipeline incorporating deep phenotyping, variant filtering, and interpretation tools in patients unsolved following coding variant analysis. Variant effects were confirmed where possible using molecular biology techniques.

Results : Our analysis pipeline identified candidate pathogenic structural and non-coding variants in the ABCA4, BEST1, CHM, CRB1, EYS, GUCY2D, IFT140, PDE6B, PRPF31 and USH2A genes. These variants included: 1. Splice region and deep intronic single nucleotide variants that result in altered splicing by weakening existing splice sites or creating cryptic splice sites. 2. Upstream gene regulatory region variants that alter the level of gene transcription through changes in transcription factor binding sites. 3. An entirely intronic complex structural rearrangement in the CHM gene comprising a 5 kilobase deletion and a 220 base inversion at the 3’ breakpoint, predicted to lead to an altered transcript. 4. Variants affecting the canonical splice-site of the non-coding first exons of the PRPF31 and BEST1 genes.

Conclusions : Implementation of WGS in a clinical genomic pipeline enables detection and interpretation of potential pathogenic variants across the entire genomic footprint of a diagnostic gene panel. We report newly identified variants otherwise missed by exon-focused diagnostic strategies that account for a significant proportion of missing heritability in IRD. In silico and functional investigation confirmed the pathogenicity of these variants and should be integrated in future clinical diagnostic pipelines incorporating WGS screening.

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