Gene Discovery in the Human Visual System

Abstract

Abstract: : Purpose: Identification of a non–redundant set of eye–expressed genes from sub–regions expected to be poorly represented in previously sequenced eye libraries. Methods: A cDNA–based gene discovery project was performed using specific sub–regions of the eye, and normalization and serial subtraction of cDNA libraries. The sequences generated were analyzed with our locally developed EST processing pipeline. Results: We have created a unique resource for research within the visual system. More than 50,000 3’ ESTs (expressed sequence tags) and their corresponding 5’ ESTs have been generated from normalized and subtracted cDNA libraries derived from (i) RPE and choroid, (ii) foveal and macular retina, (iii) whole retina, (iv) optic nerve, (v) anterior segment, (vi) lens, and (vii) fetal eye. This set of sequences represents approximately half of all eye–derived ESTs present in dbEST, and defines a non–redundant set of 14,742 UniGene clusters. More than four thousand of these are only known to be expressed in eye based upon the UI eye EST set. Of these, 407 of these clusters are composed only of ESTs from these sequences. Importantly 1463 of these UniGene clusters are not represented in the Affymetrix U133 gene chip. These sequences have been submitted to GenBank and are also available through our web–site (genome.uiowa.edu) Conclusions: This research generated approximately 100,000 eye–derived ESTs, and identified approximately 15,000 eye–expressed genes. This information will provide added benefit in identifying and prioritizing candidate disease genes.

Keywords: retina • retinal pigment epithelium • choroid