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Marina Riera, Rafael Navarro, Sheila Ruiz-Nogales, Pilar Mendez, Anniken Bures-Jelstrup, Borja Corcostegui, Esther Pomares; Ion Proton system enables reliable genetic diagnosis and improves mutation detection rate of inherited retinal dystrophies. Invest. Ophthalmol. Vis. Sci. 2017;58(8):2757.
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© ARVO (1962-2015); The Authors (2016-present)
Inherited retinal dystrophies (IRD) comprise a wide group of clinically and genetically complex diseases that progressively affect the retina. Over recent years, the development of next-generation sequencing (NGS) methods has transformed our ability to diagnose these heterogeneous diseases. In this study, we have evaluated the implementation of whole exome sequencing (WES) for the molecular diagnosis of IRD.
A total of 59 unrelated families affected by different IRD subtypes were included in the study. Ion AmpliseqTM Exome technology and Ion ProtonTM platform allowed for the capturing, amplification and sequencing of the coding regions of >19,000 genes. The generated data was filtered to obtain the variants of 212 genes responsible for more than 25 syndromic and non-syndromic IRD. Detected variants were selected according to coverage, minor allele frequency, and deleterious potential. For some particular cases, pathogenicity was further assessed by in vivo functional studies, which were carried out from patient’s RNA blood samples.
A total of 5,294 amplicons covered 98.4% of the coding regions and flanking exon/intron boundaries of the IRD genes. On average, depth coverage was 121x, with only 3% of the target regions showing values <20x. After the genotyping, we found 63 different mutations (21 of them novel) in 29 distinct genes. The causative variant was identified in 71.18% of the families (42/59). Interestingly, the mutation detection rate varied substantially depending on the IRD subtype. In addition, functional studies confirmed the deleterious impact of variants identified in CDHR1, MERTK, CDH23 and RPGRIP1.
In conclusion, we analyzed a large cohort of clinically heterogeneous IRD patients using WES and report a diagnostic yield greater than 70%, which is higher than most previous studies. The improvement displayed in our study may be explained by different factors: i) a more accurate clinical characterization; ii) superior gene panel design; iii) a more optimal data analysis pipeline; and iv) better coverage of the genes of interest. Altogether, our results indicate that WES using Ion ProtonTM system is a reliable, hypothesis-free approach, and a cost- and time-effective strategy for the routine genetic diagnosis of retinal dystrophies.
This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.
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