Identification of candidate retinal degeneration genes by genome wide EST mapping

Abstract

Abstract: : Purpose:Progressive Retinal Atrophy (PRA) in dogs and Retinitis Pigmentosa (RP) in humans are clinically similar genetic diseases, each comprising multiple specific disorders mapping to different chromosomal regions. Identification of the causative mutations, however, is often limited by our restricted understanding of potential candidate genes located in those areas. Using a canine retinal EST library described previously, we aimed to increase the density of the canine map specifically for novel retinal expressed cDNAs. Because of the well established conserved syntenies between the dog and human, this approach will identify new potential disease candidate genes for both species. Methods:Retinal EST mapping was performed on the RHDF₅₀₀₀ canine/hamster hybrid panel using previously published markers as reference points (Guyon et al., 2003). Linkage groups were identified and ordered using Multimap software. Results:An initial set of 1,418 primer pairs were designed from thus far unidentified canine retinal ESTs, of which 999 (70%) amplified from canine genomic DNA. A subset of 556 (56%), each representing an independent EST cluster, amplified a unique product specific for canine DNA on the dog/hamster hybrid panel. Using these, we were able to locate 553 canine retinal ESTs within the canine genome, ranging from 3 (CFA32, CFY) to 35 (CFA1) ESTs per chromosome. As a test of this approach, we identified 5 novel potential candidate genes mapping to the prcd interval on CFA9. Conclusions:Mapping data for the retinal ESTs generated through this project will be valuable for both the ongoing canine genome project and our canine retinal EST database, and provides a powerful resource to identify novel genes potentially involved in retinal development and degeneration in both the dog and humans.

Keywords: gene mapping • retinal degenerations: hereditary • linkage analysis