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Stephen Daiger, Lori Sullivan, Sara Bowne, George Weinstock, Daniel Koboldt, Rui Chen, John Heckenlively, Kari Branham, David Birch, Dianna Wheaton; Application of Whole-Exome and Retinal-Capture Next-Generation DNA Sequencing to Identify Disease-Causing Mutations in Families with a Diagnosis of Autosomal Dominant Retinitis Pigmentosa. Invest. Ophthalmol. Vis. Sci. 2013;54(15):4974.
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To detect disease-causing mutations in families with a diagnosis of autosomal dominant retinitis pigmentosa (adRP), focusing on genes known to cause inherited retinal diseases, using whole-exome next-generation sequencing (NGS) and retinal-capture NGS.
Families were selected from a cohort of 260 with a diagnosis of adRP and 3 affected generations and affected females, or two generations with male-to-male transmission. The families were previously screened for common mutations by Sanger sequencing. Coding exons and flanking intron-exon junctions of all known RetNet genes and candidate genes were targeted for NGS. Testing was either 1.) whole-exome NGS using Agilent SureSelect liquid-capture probes and the Illumina platform, focusing analysis on 190 retinal disease genes, 2.) targeted liquid-capture and NGS of coding regions of 160 retinal disease genes, or 3.) both. Families tested included positive controls with known mutations and families without a previously-identified mutation. Mutations detected by NGS were confirmed by Sanger sequencing.
Probands and additional family members from 87 families, including controls, were tested by one or both methods. Of 22 families tested by whole-exome NGS, mutations were found in 7 (32%). Of 18 control families with known mutations tested by retinal-capture NGS, mutations were found in 17. (A large deletion in PRPF31 was not detected). Of 69 families without known mutations tested by retinal-capture NGS, mutations were found in 10 (15%). In summary, of a total of 76 families whose mutations were not known prior to NGS, mutations were found in 17 (22%). Several of these mutations are in genes not currently associated with autosomal dominant disease.
Targeted retinal-gene capture or focused retinal-gene analysis following whole-exome NGS, are reliable, efficient methods for detecting disease-causing mutations in families with dominant retinitis pigmentosa. Based on a variety of methods, mutations in coding exons or intron-exon junctions of known retinal disease genes (RetNet genes) account for at least 72% of families in our cohort with dominant RP.
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