Novel RP1 mutations and a recurrent BBS1variant explain the co-existence of two distinct retinal phenotypes in the same pedigree

Abstract

BackgroundMolecular diagnosis of Inherited Retinal Dystrophies (IRD) has long been challenging due to the extensive clinical and genetic heterogeneity present in this group of disorders. Here, we describe the clinical application of an integrated next-generation sequencing approach to determine the underlying genetic defects in a Spanish family with a provisional clinical diagnosis of autosomal recessive Retinitis Pigmentosa (arRP).ResultsExome sequencing of the index patient resulted in the identification of the homozygous BBS1 p.M390R mutation. Sanger sequencing of additional members of the family showed lack of co-segregation of the p.M390R variant in some individuals. Clinical reanalysis indicated co-ocurrence of two different phenotypes in the same family: Bardet-Biedl syndrome in the individual harboring the BBS1 mutation and non-syndromic arRP in extended family members. To identify possible causative mutations underlying arRP, we conducted disease-targeted gene sequencing using a panel of 26 IRD genes. The in-house custom panel was validated using 18 DNA samples known to harbor mutations in relevant genes. All variants were redetected, indicating a high mutation detection rate. This approach allowed the identification of two novel heterozygous null mutations in RP1 (c.4582_4585delATCA; p.I1528Vfs*10 and c.5962dupA; p.I1988Nfs*3) which co-segregated with the disease in arRP patients. Additionally, a mutational screening in 96 patients of our cohort with genetically unresolved IRD revealed the presence of the c.5962dupA mutation in one unrelated family.ConclusionsThe combination of molecular findings for RP1 and BBS1 genes through exome and gene panel sequencing enabled us to explain the co-existence of two different retinal phenotypes in a family. The identification of two novel variants in RP1 suggests that the use of panels containing the prevalent genes of a particular population, together with an optimized data analysis pipeline, is an efficient and cost-effective approach that can be reliably implemented into the routine diagnostic process of diverse inherited retinal disorders. Moreover, the identification of these novel variants in two unrelated families supports the relatively high prevalence of RP1 mutations in Spanish population and the role of private mutations for commonly mutated genes, while extending the mutational spectrum of RP1.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0143-2) contains supplementary material, which is available to authorized users.

Macular Dystrophy and Cone-Rod Dystrophy Caused by Mutations in theRP1Gene: Extending theRP1Disease Spectrum

“…23 In addition, other previously reported variants, such as p.D202E, p.I1988Nfs*3, and p.I2061Sfs*12, could also be predicted to be mild or hypomorphic variants considering their location; however, they have been associated with arRP, although the clinical phenotype has not been described in detail. [23][24][25] The explanation for this clinical heterogeneity remains to be elucidated, but might be explained by additional (genetic-) modifying factors, the presence of a structural variant or a variant in the non-coding regions of RP1, pathogenic variants in another RP gene, or inaccurate phenotyping, the latter of which should be considered particularly in advanced RP and CRD, in which the distinction can be difficult and depends on patients' self-reported disease course. A potential genetic modifier for RP1-associated disease may be RP1L1, because these proteins have synergistic roles in the photoreceptor axoneme.…”

Improving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel

“…In order to identify causative mutations in the sequenced samples, we used our validated data analysis pipeline 29 with some modifications. Sequence reads were mapped against the human genome reference (hg19) using SureCall software (Agilent, version 2.1).…”

Re‐evaluation casts doubt on the pathogenicity of homozygous USH2A p.C759F

“…Written informed consent was obtained from all participants. Clinical diagnosis of ARRP was ascertained as described [Mendez-Vidal et al, 2014]. Individual II:1 underwent ophthalmogic examination including fundoscopy and electroretinography.…”

“…Library preparation, targeted sequencing on a 454 Roche GS Junior sequencer and data analysis were performed as described [Mendez-Vidal et al, 2014].…”

“…According to the relatively high prevalence of the p.C759F variant and the discrepancies between clinical data and genetic findings in family S23, we set out to evaluate the pathogenicity of this variant using a NGS panel of 26 retinal genes [Mendez-Vidal et al, 2014].…”