Whole-Exome Analysis for Polish Caucasian Patients with Retinal Dystrophies and the Creation of a Reference Genomic Database for the Polish Population

Abstract

We present the results of the first study of a large cohort of patients with inherited retinal dystrophies (IRD) performed for the Polish population using whole-exome sequencing (WES) in the years 2016-2019. Moreover, to facilitate such diagnostic analyses and enable future application of gene therapy and genome editing for IRD patients, a Polish genomic reference database (POLGENOM) was created based on whole-genome sequences of healthy Polish Caucasian nonagenarians and centenarians. The newly constructed database served as a control, providing a comparison for variant frequencies in the Polish population. The diagnostic yield for the selected group of IRD patients reached 64.9%. The study uncovered the most common pathogenic variants in ABCA4 and USH2A in the European population, along with several novel causative variants. A significant frequency of the ABCA4 complex haplotype p.(Leu541Pro; Ala1038Val) was observed, as well as that of the p.Gly1961Glu variant. The first VCAN causative variant NM_004385.5:c.4004-2A>G in Poland was found and described. Moreover, one of the first patients with the RPE65 causative variants was identified, and, in consequence, could receive the dedicated gene therapy. The availability of the reference POLGENOM database enabled comprehensive variant characterisation during the NGS data analysis, confirming the utility of a population-specific genomic database for enhancing diagnostic accuracy. Study findings suggest the significance of genetic testing in elder patients with unclear aetiology of eye diseases. The combined approach of NGS and the reference genomic database can improve the diagnosis, management, and future treatment of IRDs.

Keywords: WES; WGS; inherited retinal dystrophy; population database; retinitis pigmentosa.

Figure 1

Distribution of genes with confirmatory variants among 50 distinct solved patients (total number of patients with confirmatory variants in the denoted gene in brackets).

Figure 2

Distribution of genes with confirmatory variants among distinct solved patients in the two groups: (a) unspecific IRD group; (b) RP group. Total number of patients with confirmatory variants in the denoted gene in brackets.

Figure 3

Ultrawidefield eye fundus images (Optos) - VCAN-related Wagner syndrome family: patient S48, father, 52 years old: (a) (right eye, RE), (b) (left eye, LE); patient S46, son, 20 years old (c) (LE), (d) (RE); (e) Sanger confirmation of the NM_004385.5:c.4004-2A>G variant in VCAN for patient S46 (top), patient S48 (middle), and wild-type control sample (bottom). Due to changes involving the anterior segment of the eye in the father, with extensive phimosis of the lens capsule after cataract surgery, fundus imaging is difficult. In this case, widefield images cover a limited area of the retina; in the right eye, only the nasal part of the retina is visible (a). Pigmentary changes located mainly on the periphery of the retina resemble retinitis pigmentosa, which was the first, initial diagnosis in both father and son. Visual acuity was low at 0.01 (RE), 0.05 (LE), but stable for the last 10 years. In his son, pigmentary and atrophic changes were less severe. The boundary line of the optically empty part of the vitreous body was clearly marked, from which vitreoretinal tractions extend towards the periphery. Best corrected visual acuity is 1.0 (RE) and 0.9 (LE), but with a narrowed field of vision. Snellen charts were used for visual acuity examination.