Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements

Abstract

Retinitis pigmentosa (RP) is a devastating form of retinal degeneration, with significant social and professional consequences. Molecular genetic information is invaluable for an accurate clinical diagnosis of RP due to its high genetic and clinical heterogeneity. Using a gene capture panel that covers 163 of the currently known retinal disease genes, including 48 RP genes, we performed a comprehensive molecular screening in a collection of 123 RP unsettled probands from a wide variety of ethnic backgrounds, including 113 unrelated simplex and 10 autosomal recessive RP (arRP) cases. As a result, 61 mutations were identified in 45 probands, including 38 novel pathogenic alleles. Interestingly, we observed that phenotype and genotype were not in full agreement in 21 probands. Among them, eight probands were clinically reassessed, resulting in refinement of clinical diagnoses for six of these patients. Finally, recessive mutations in CLN3 were identified in five retinal degeneration patients, including four RP probands and one cone-rod dystrophy patient, suggesting that CLN3 is a novel non-syndromic retinal disease gene. Collectively, our results underscore that, due to the high molecular and clinical heterogeneity of RP, comprehensive screening of all retinal disease genes is effective in identifying novel pathogenic mutations and provides an opportunity to discover new genotype-phenotype correlations. Information gained from this genetic screening will directly aid in patient diagnosis, prognosis, and treatment, as well as allowing appropriate family planning and counseling.

Fig. 1

High quality sequencing results were obtained. (a) The solid curve shows the fraction of targeted region (y-axis) covered by at least certain coverage (x-axis). Dashed lines show the 95% confidence interval. (b) The evenness score of capture sequencing results from 123 RP samples

Fig. 2

Automatic pipeline used to filter and annotate variants

Fig. 3

Pedigrees and mutations segregating in family 3812 (a) and family 1467 (b)

Fig. 4

Fundus images of proband 3812. Shown are (a) fundus photograph, (b) fundus autofluorescence (FAF) and (c) optical coherence tomography (OCT) images. The images of OS reveal an extensive maculopathy in a horsehoe pattern, with absent FAF pericentrally and marked retinal remodelling with extensive debris and CME in the fovea

Fig. 5

Pedigrees and mutations segregating in family 2055 (a), family 348 (b), family 2044 (c), family 2691 (d) and family SRF41 (e)

Fig. 6

Fundus images of proband 2055. Shown are (a) fundus photograph, (b) fundus autofluorescence (FAF) and (c) optical coherence tomography (OCT) images. The retinal photograph of the OS shows mild choroidal sclerosis and peripheral pigment mottling. FAF shows a central hyper-fluorescent ring surrounded by essentially normal FAF, surrounded by mottled FAF outside the arcades. OCT shows extensive IS/OS junction loss, except in the fovea