Identifying and Annotating Disease Specific Rat Genome Sequences

Jedidiah Mathis1, Mary Shimoyama2, Aubrey Hughes, Norberto Dela Cruz, Charles Wang, Simon Twigger, Michael Jensen-Seamen, Michelle Feldmann, Artur Rangel Filho, Jozef Lazar, Howard Jacob, Peter Tonellato, Medical College of Wisconsin;, Medical College of Wisconsin

Eleven disease related Genomic Regions Of Interest (GROI) were submitted to the Rat Genome Sequencing Consortium for prioritized sequencing. These eleven GROIs are composed of disease related QTLs and some of the regions contain several QTLs. In total the eleven GROIs cover approximately ten percent of the rat genome. The GROIs were sequenced to a greater depth of coverage than the rest of the rat genome. We analyzed these highly sequenced areas to determine whether greater coverage facilitated denser and more accurate annotation. The eleven GROIs were compared with comparable regions as well as the genome as a whole in terms of number of predicted and known genes, organization of genes in relationship to existing RH and Genetic maps, and functional annotation. Functional annotation included such data as expression, tissue, pathway, homologs, syntenic regions in the mouse and human, related QTLs from human mouse and rat, gene product, gene function, related strains, SNPs, related biomedical literature and Gene Ontology (GO) associations. Annotation was achieved using a combination of datamining of public databases and manual curation. Resulting datasets provide the researcher with a detailed view of the genomic regions of interest that facilitate identification of candidate genes. Incorporation of this annotation into a genome browser environment provides researchers with a tool for mapping disease to the genome.