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S. Amer Riazuddin, Nicholas Katsanis, John D. Gottsch; Next Generation Sequencing to Identify the Genetic Basis of late-onset Fuchs Corneal Dystrophy. Invest. Ophthalmol. Vis. Sci. 2011;52(14):1107.
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Fuchs Corneal Dystrophy (FCD) is a common progressive disorder of the corneal endothelium that affects as much as 4% of the United States population over the age of 40 years. Previously, we localized late-onset FCD in three large families with multiple affected individuals to chromosome 18q but the causal lesion responsible for the disease phenotype in these three families is yet unknown. This study was designed to identify the genetic basis of late-onset FCD utilizing the next-generation sequencing by synthesis technology.
We reassigned the proximal and distal boundaries of the FCD2 locus based on at least two recombination events at each end. Exonic regions of all UCSC genes along with 20 base pair of sequence from the 5` and 3` ends of these exons were designed on a 385K Nimblegen array. Targeted regions from one affected and an unaffected individual per family were captured, enriched, and pair-end sequenced on an Illumina IIx genome analyzer. The raw data were assembled by Eland algorithms and aligned to the chromosome 18 reference sequence by Seqmate software.
The reassignment of the proximal and distal boundaries extended the critical interval to a 27 Mb region. Paired-end sequencing generated on average 1.2 GB data per sample corresponding to approximately 35 million reads of 36 bp length. The overall sequencing depth averaged to 85x with only a small fraction (2%) of targeted region attained less than 25x coverage. Majority (>90) of the variants identified in each these samples were single nucleotide polymorphisms, whereas 73 variants were unique to the affecteds and were absent in the unaffected individuals of the FCD2-linked families.
A total of 26,877 variants were identified in six samples from the three FCD2-linked families. Currently, we are investigating the significance of these variants and their potential involvement in the pathogenesis of late-onset FCD. Identification of the pathogenic mutations responsible for the disease phenotype will help us better understand the causality of the late-onset FCD at a molecular level.
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