Findings from a Genotyping Study of Over 1000 People with Inherited Retinal Disorders in Ireland

Abstract

The Irish national registry for inherited retinal degenerations (Target 5000) is a clinical and scientific program to identify individuals in Ireland with inherited retinal disorders and to attempt to ascertain the genetic cause underlying the disease pathology. Potential participants first undergo a clinical assessment, which includes clinical history and analysis with multimodal retinal imaging, electrophysiology, and visual field testing. If suitable for recruitment, a sample is taken and used for genetic analysis. Genetic analysis is conducted by use of a retinal gene panel target capture sequencing approach. With over 1000 participants from 710 pedigrees now screened, there is a positive candidate variant detection rate of approximately 70% (495/710). Where an autosomal recessive inheritance pattern is observed, an additional 9% (64/710) of probands have tested positive for a single candidate variant. Many novel variants have also been detected as part of this endeavor. The target capture approach is an economic and effective means of screening patients with inherited retinal disorders. Despite the advances in sequencing technology and the ever-decreasing associated processing costs, target capture remains an attractive option as the data produced is easily processed, analyzed, and stored compared to more comprehensive methods. However, with decreasing costs of whole genome and whole exome sequencing, the focus will likely move towards these methods for more comprehensive data generation.

Keywords: genomics; inherited eye disease; next generation sequencing; novel variants; ophthalmic genetics; rare variants; retinopathy.

Figure 1

Clinical presentation of 1004 recruited Target 5000 pedigrees. RP: Retinitis Pigmentosa, FFM: Fundus Flavimaculatus, MD: Macular Dystrophy, CRD: Cone-Rod Dystrophy, RCD: Rod-Cone Dystrophy, LCA: Leber Congenital Amaurosis, EOSRD: Early-Onset Retinal Degeneration, BBS: Bardet-Biedl Syndrome, CSNB: Congenital Stationary Night Blindness (Table S2).

Figure 2

Diagnostic yield rates for 710 Target 5000 pedigrees utilising target capture next-generation sequencing of the exonic regions of over 250 genes and previously identified pathogenic intronic variants (Table S3).

Figure 3

A summary of the genetic architecture of retinitis pigmentosa (RP) in Target 5000 participants (Table S4).

Figure 4

Collage of fundus images of a patient initially presenting with a Stargardt phenotype that progressed to phenotype suggestive of retinitis pigmentosa. Extensive pigmentation can be seen at both maculae and also in the periphery of both eyes (left—right eye, right—left eye). There are also distinct punched-out areas in the pigment epithelium bilaterally.

Figure 5

Montage of autofluorescence fundus images of the patients initially presenting with a Stargardt phenotype that progressed to phenotype suggestive of retinitis pigmentosa. The right eyes are shown in the left column; the left eyes are shown in the right column. Patient example 1 is the first row and patient example 2 is the second row. All eyes demonstrate a dark choroid and large nummular regions of hypoautofluorescence throughout the retinae.

Figure 6

A summary of the genetic architecture of macular dystrophies in Target 5000 participants. CRD: Cone-Rod Dystrophy FA: Fundus Albipunctatus (Table S5).

Figure 7

A summary of the genetic architecture of Usher Syndrome (USH) in Target 5000 participants (Table S6).

Figure 8

A summary of the genetic architecture of less common phenotypes encountered in the Target 5000 study. LCA: Leber Congenital Amaurosis, LHON: Leber Hereditary Optic Neuropathy (Table S7).

Figure 9

An illustration of patients harbouring the RPE65 c.1430A>G (p.D477G) variant. In this pedigree, each individual’s phenotype corresponds to the expected genotype (left image). Also shown is a representative Sanger sequence trace from an unaffected (wild-type) family member (right image, top). The variant sequence shown below is that from an affected family member (right image, bottom). Sequences were read from the sense strand so the observed change above is T>G (GGCA[T>G]CTG).

Figure 10

Montage of wide-field fundus images from a retinitis pigmentosa patient with a FLVCR1 genotype. The FLVCR1 genotype results in a phenotype (left- right eye, right- left eye) that appears to bear a resemblance to classical retinitis pigmentosa, with features such as masses of bony spicules in the periphery, attenuated blood vessels, and waxy disc pallor. There is also a relative preservation of the maculae.

Figure 11

Schematic representation of the genomic region surrounding the CHM gene. Whole-genome coverage data from a control population database (https://gnomad.broadinstitute.org/). Structural variants detected from controls samples and Target 5000 patients are aligned to this region to illustrate the instability of this genomic region. Blue = duplication, Red = deletion, Pink = template positive results likely due to highly similar sequence elsewhere in the genome.

Figure 12

Partial pedigree tree illustrating the segregation of two X-linked retinal conditions within one family.