Detailed analysis of an enriched deep intronic ABCA4 variant in Irish Stargardt disease patients

Over 15% of probands in a large cohort of more than 1500 inherited retinal degeneration patients present with a clinical diagnosis of Stargardt disease (STGD1), a recessive form of macular dystrophy caused by biallelic variants in the ABCA4 gene. Participants were clinically examined and underwent either target capture sequencing of the exons and some pathogenic intronic regions of ABCA4, sequencing of the entire ABCA4 gene or whole genome sequencing. ABCA4 c.4539 + 2028C > T, p.[= ,Arg1514Leufs*36] is a pathogenic deep intronic variant that results in a retina-specific 345-nucleotide pseudoexon inclusion. Through analysis of the Irish STGD1 cohort, 25 individuals across 18 pedigrees harbour ABCA4 c.4539 + 2028C > T and another pathogenic variant. This includes, to the best of our knowledge, the only two homozygous patients identified to date. This provides important evidence of variant pathogenicity for this deep intronic variant, highlighting the value of homozygotes for variant interpretation. 15 other heterozygous incidents of this variant in patients have been reported globally, indicating significant enrichment in the Irish population. We provide detailed genetic and clinical characterization of these patients, illustrating that ABCA4 c.4539 + 2028C > T is a variant of mild to intermediate severity. These results have important implications for unresolved STGD1 patients globally with approximately 10% of the population in some western countries claiming Irish heritage. This study exemplifies that detection and characterization of founder variants is a diagnostic imperative.

Target 5000: a standardized all-Ireland pathway for the diagnosis and management of inherited retinal degenerations

Introduction

Inherited retinal degenerations (IRD) are rare genetic disorders with > 300 known genetic loci, manifesting variably progressive visual dysfunction. IRDs were historically underserved due to lack of effective interventions. Many novel therapies will require accurate diagnosis (phenotype and genotype), thus an efficient and effective pathway for assessment and management is required.

Methods

Using surveys of existing practice patterns and advice from international experts, an all-Ireland IRD service (Target 5000) was designed. Detailed phenotyping was followed by next generation genetic sequencing in both a research and accredited laboratory. Unresolved pedigrees underwent further studies (whole gene/whole exome/whole genome sequencing). Novel variants were interrogated for pathogenicity (cascade screening, in silico analysis, functional studies). A multidisciplinary team (MDT; ophthalmologists, physicians, geneticists, genetic counsellors) reconciled phenotype with genotype. A bespoke care plan was created for each patient comprising supports, existing interventions, and novel therapies/clinical trials.

Results and discussion

Prior to Target 5000, a significant cohort of patients were not engaged with healthcare/support services due to lack of effective interventions. Pathogenic or likely pathogenic variants in IRD-associated genes were detected in 62.3%, with 11.6% having variants of unknown significance. The genotyping arm of Target 5000 allowed a 42.73% cost saving over independent testing, plus the value of MDT expertise/processing. Partial funding has transferred from charitable sources to government resources.

Conclusion

Target 5000 demonstrates efficacious and efficient clinical/genetic diagnosis, while discovering novel IRD-implicated genes/variants and investigating mechanisms of disease and avenues of intervention. This model could be used to develop similar IRD programmes in small/medium-sized nations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-021-01841-1.

A Case Series of "Solitary Idiopathic Choroiditis" and Proposal of a Nomenclature Change to "Idiopathic Scleroma"

Objective

To define the characteristics of solitary idiopathic choroiditis (SIC) in a consecutive series of patients and propose a nomenclature change to idiopathic scleroma.

Materials and Methods

Electronic patient records were retrospectively interrogated to identify all patients diagnosed with SIC between 2002 and 2019 in a tertiary referral ophthalmic hospital in the United Kingdom.

Results

Thirty-four eyes of 34 patients were found to have SIC. The mean age at diagnosis was 48 years (range 24-78) and 23 patients (68%) were female. All lesions were located posterior to the equator, most frequently in the inferotemporal quadrant (13 eyes, 38%). The lesions had a mean largest basal diameter of 1.2 ± 0.4 disc diameters (range 0.5-2) and their distance to the optic disc had a mean of 1.2 ± 0.9 disc diameters (range 0-3.3). All lesions were intrascleral on enhanced depth imaging optical coherence tomography, demonstrating a hypo-reflective zone within the sclera, with an underlying hyper-reflective zone in some cases. No lesion enlarged or developed features consistent with active inflammation after a median follow-up time of 0.9 years (range 0-16.8).

Discussion/Conclusion

Optical coherence tomography shows SIC to be an intrascleral lesion. Furthermore, we found no evidence of any inflammatory component. A nomenclature change to idiopathic scleroma is appropriate to prevent unnecessary investigation.

Panel-Based Population Next-Generation Sequencing for Inherited Retinal Degenerations

Inherited retinopathies affect approximately two and a half million people globally, yet the majority of affected patients lack clear genetic diagnoses given the diverse range of genes and mutations implicated in these conditions. We present results from a next-generation sequencing study of a large inherited retinal disease patient population, with the goal of providing clear and actionable genetic diagnoses. Targeted sequencing was performed on 539 individuals from 309 inherited retinal disease pedigrees. Causative mutations were identified in the majority (57%, 176/309) of pedigrees. We report the association of many previously unreported variants with retinal disease, as well as new disease phenotypes associated with known genes, including the first association of the SLC24A1 gene with retinitis pigmentosa. Population statistics reporting the genes most commonly implicated in retinal disease in the cohort are presented, as are some diagnostic conundrums that can arise during such studies. Inherited retinal diseases represent an exemplar group of disorders for the application of panel-based next-generation sequencing as an effective tool for detection of causative mutations.

A novel homozygous truncating GNAT1 mutation implicated in retinal degeneration

Background

The GNAT1 gene encodes the α subunit of the rod transducin protein, a key element in the rod phototransduction cascade. Variants in GNAT1 have been implicated in stationary night-blindness in the past, but unlike other proteins in the same pathway, it has not previously been implicated in retinitis pigmentosa.

Methods

A panel of 182 retinopathy-associated genes was sequenced to locate disease-causing mutations in patients with inherited retinopathies.

Results

Sequencing revealed a novel homozygous truncating mutation in the GNAT1 gene in a patient with significant pigmentary disturbance and constriction of visual fields, a presentation consistent with retinitis pigmentosa. This is the first report of a patient homozygous for a complete loss-of-function GNAT1 mutation. The clinical data from this patient provide definitive evidence of retinitis pigmentosa with late onset in addition to the lifelong night-blindness that would be expected from a lack of transducin function.

Conclusion

These data suggest that some truncating GNAT1 variants can indeed cause a recessive, mild, late-onset retinal degeneration in human beings rather than just stationary night-blindness as reported previously, with notable similarities to the phenotype of the Gnat1 knockout mouse.

Mohs micrographic surgery for periocular skin tumours in Ireland

OBJECTIVE

To describe the shared care and outcomes of patients with periocular skin tumours who underwent Mohs micrographic surgery (MMS) performed by dermatologists, followed by oculoplastic reconstruction undertaken by ophthalmologists at two teaching and one private hospital in Ireland.

RESEARCH DESIGN AND METHODS

This was a retrospective chart review at the Royal Victoria Eye and Ear Hospital, St James Hospital and the Hermitage Clinic.

RESULTS

One hundred and twenty seven patients had periocular Mohs surgery between November 2006 and January 2013 mainly indicated for basal cell carcinoma. The mean follow-up time was 2 years and to date there have been no local recurrences.

CONCLUSIONS

MMS is available in Ireland and should be considered for patients with facial tumours in the ocular region.

Ophthalmic manifestations of vitamin A and D deficiency in two autistic teenagers: case reports and a review of the literature

We describe the cases of 2 autistic children with ophthalmic and systemic manifestations of vitamin A deficiency due to food faddism. Although vitamin A deficiency is common in the developing world, reports in developed societies are rare. Our patients presented over a 1-year period. The patients were 14 and 13 years old at the time of presentation and were both found to have marked features of vitamin A deficiency related to unusual dietary habits. Anterior segment signs of xerophthalmia were present in both patients. In addition, patient 1 showed evidence of a rod-predominant retinopathy, which resolved with vitamin A supplementation. Due to its rare occurrence, hypovitaminosis A must be highlighted and anticipated in this cohort.