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E.M. Stone, R.E. Swiderski, K.Y. Kim, A.R. Philp, K.L. Knudtson, G. DiBona, J. Huang, V.C. Sheffield; Genome–Wide Genetic Analysis of Gene Expression Variation in the Mammalian Eye . Invest. Ophthalmol. Vis. Sci. 2005;46(13):2390.
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© ARVO (1962-2015); The Authors (2016-present)
Purpose: The long term goal of this project is to gain a broad perspective of mechanisms of gene regulation in the mammalian eye and to use this improved perspective to find new genes that cause human eye disease. Recent advances in microarray technology and bioinformatics have made it possible to perform experiments that examine the expression of thousands of genes in large numbers of related individuals and to use these data to identify the chromosomal locations of the genetic elements that are responsible for the variation in gene expression among individuals. This technique is known as "expression quantitative trait locus mapping" (often abbreviated as "eQTL mapping"). Methods: Two inbred strains of laboratory rats (SR/JR/HSD and SHR/SP) were crossed and the resultant F1 animals were inter–crossed. At 12 weeks of age, 120 healthy males of the resulting F2 generation were euthanized. RNA was extracted from the eyes and genomic DNA was extracted from the liver of each animal. The ocular gene expression of each animal was determined using Affymetrix microarrays (GeneChip Rat Genome 230 2.0 Arrays – containing 31000 probes). Each animal was genotyped with 100 fully informative genetic markers distributed across the entire rat genome. Genetic analysis was performed to look for a relationship between each genetic marker and each probe represented on the microarray. Results: Of the 31000 probes represented on the microarray, 18000 exhibited sufficient signal for reliable analysis as well as at least 2 fold variation in expression among the 120 F2 animals. Linkage analysis of the first 100 markers revealed significant linkage with at least one genetic marker for 1700 probes (p < 0.0001, estimated empirical false discovery rate < 0.10). The distribution of the number of significant probes across the genome was non–uniform suggesting the existence of master loci that influence the regulation of multiple genes. Furthermore, the data indicate that both trans– and cis–acting loci are important in regulating mammalian eye gene expression. Conclusions: This study demonstrates that genetic variation is responsible for a large amount of gene expression variation, and also demonstrates the feasibility of large scale mapping of loci that regulate gene expression in the mammalian eye. Additional analyses of the data will allow the identification of both individual and interacting loci regulating expression of specific genes. These data should contribute to a better understanding of normal and abnormal ocular physiology.
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