Diagnostic application of clinical exome sequencing in Leber congenital amaurosis

Abstract

Purpose: Leber congenital amaurosis (LCA) is a hereditary retinal dystrophy with wide genetic heterogeneity. Next-generation sequencing (NGS) targeting multiple genes can be a good option for the diagnosis of LCA, and we tested a clinical exome panel in patients with LCA.

Methods: A total of nine unrelated Korean patients with LCA were sequenced using the Illumina TruSight One panel, which targets 4,813 clinically associated genes, followed by confirmation using Sanger sequencing. Patients' clinical information and familial study results were obtained and used for comprehensive interpretation.

Results: In all nine patients, we identified pathogenic variations in LCA-associated genes: NMNAT1 (n=3), GUCY2D (n=2), RPGRIP1 (n=2), CRX (n=1), and CEP290 or SPATA7. Six patients had one or two mutations in accordance with inheritance patterns, all consistent with clinical phenotypes. Two patients had only one pathogenic mutation in recessive genes (NMNAT1 and RPGRIP1), and the clinical features were specific to disorders associated with those genes. Six patients were solved for genetic causes, and it remains unclear for three patients with the clinical exome panel. With subsequent targeted panel sequencing with 113 genes associated with infantile nystagmus syndrome, a likely pathogenic allele in CEP290 was detected in one patient. Interestingly, one pathogenic variant (p.Arg237Cys) in NMNAT1 was present in three patients, and it had a high allele frequency (0.24%) in the general Korean population, suggesting that NMNAT1 could be a major gene responsible for LCA in Koreans.

Conclusions: We confirmed that a commercial clinical exome panel can be effectively used in the diagnosis of LCA. Careful interpretation and clinical correlation could promote the successful implementation of clinical exome panels in routine diagnoses of retinal dystrophies, including LCA.

Figure 1

Color photographs of the retinas of six patients with LCA. A, B: Two 6-month-old babies (P2 and P3) with compound heterozygous mutations in GUCY2D (p.[Phe993LeufsTer13]+[Gly1013Glu] and p.[His664Pro]+[Phe883LeufsTer13], respectively) have no definite abnormal finding (OD) in the retina. C: A 7-month-old baby (P5) with compound heterozygous missense mutations in NMNAT1 (p.[Arg66Trp]+[Arg237Cys]) has marked chorioretinal atrophic changes in the macula with vessel narrowing and mild pigmentary changes (OD). D: A 1-year-old baby (P6) with only one pathogenic mutation in NMNAT1 (p.[Arg237Cys]+[?]) shows nystagmus, hyperopia, and a characteristic macular coloboma-like lesion (OS). E: An 8-month-old baby (P8) presented with poor eye contact, extinguished electroretinogram, +6.00 diopters hyperopia, slight optic disc pallor, and mild vessel narrowing (OD). We identified one frameshift mutation (p.Arg1189GlyfsTer7) in RPGRIP1. F: A 29-year-old male (P9) presented with nystagmus developed at the age of 6 years, 20/200 acuity, optic atrophy, and mild vessel attenuation (OD). Compound heterozygous mutations were identified in RPGRIP1 (p.[Tyr693Ter]+[c.2212_2215+21del]).

Figure 2

Fundus photographs of a 29-year-old male with mutations in RPGRIP1 who was initially misdiagnosed with idiopathic infantile nystagmus. He had sustained left head turn posture with left beating jerk nystagmus. Anderson-Kestenbaum surgery was performed at the age of 6 years. At the age of 29 years, his best visual acuity was 20/200 bilaterally. A, B: Fundus photography shows mild optic atrophy with retinal vessel attenuations. C, D: Spectral domain optical coherence tomography shows thinning of the inner segment and outer segment line.

Figure 3

Pedigrees of three patients with mutations in NMNAT1. These patients were nonconsanguineous, and all patients harbored a pathogenic mutation in NMNAT1 (c.709C>T; p. Arg237Cys), which was supposed to be a founder mutation in Koreans.