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MM Sohocki, AF Sorenson, G Shi; Identification of Candidate Genes for Inherited Retinal Disorders . Invest. Ophthalmol. Vis. Sci. 2002;43(13):2433.
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© ARVO (1962-2015); The Authors (2016-present)
Purpose: To date, although over 130 different genes associated with inherited retinopathy have been mapped, only half of the associated genes have been cloned. Many of the cloned retinopathy-associated genes have retina-specific, retina/pineal-specific of retinal pigment epithelium (RPE)-specific expression patterns. In 1998, we used a combination of in silico and laboratory methods to identify retina/pineal-specific genes as candidates for inherited retinal disorders. Mutations in one of the novel genes identified by this method, AIPL1, were determined to be the cause of approximately 10% of Leber congenital amaurosis. With the progress of the human genome project, the amount of data for these studies has increased substantially since our last study, and, in many cases, the precise mapping location and genomic structure of novel candidate genes can be identified now using the publicly available human genome sequence. Methods: The Institute for Genomic Research (TIGR) Human Gene Index assembles "clusters" of EST sequences that likely represent transcripts of the same gene, and it updates these clusters four times per year. The 9/14/2001 release was searched for novel candidate genes with retina-specific, retina/pineal-specific or RPE-specific expression patterns. The assembled sequence for each cluster was searched by RepeatMasker and BLAST to determine 1) whether the sequence represented a known gene and 2) the complete set of ESTs available for the candidate gene. Genes with expression patterns of interest were mapped using either Human Golden Path location (if available from TIGR), BLAST of human genome sequence or assay of a radiation hybrid panel. The resulting data were compared to published mapping locations of inherited retinopathy loci. Results: Although the analysis of the data is not complete, we have already identified a novel RPE-specific candidate gene for Leber congenital amaurosis (LCA3), and a retina-specific candidate gene for recessive retinitis pigmentosa (RP26). In addition, we have identified several known genes associated with inherited retinopathy and several novel retina-expressed genes using this method. Conclusion: This combination of in silico and laboratory analyses has proven to be a successful approach to determine candidate genes for inherited retinopathy. It is likely that identification of novel retina-expressed genes by this method will also increase our understanding of normal vision. Supported by the Kirchgessner Foundation; the Knights Templar Eye Foundation; the Foundation Fighting Blindness; and Fight for Sight, Research Division of Prevent Blindness America
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