Abstract
Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, genome manipulation. Through the innovation of genome-editing technologies, genome-modified rats provide precision models of disease by disrupting or complementing targeted genes. To facilitate the use of these data produced from rat disease models, the Rat Genome Database (RGD) organizes rat strains and annotates these strains with disease and qualitative phenotype terms as well as quantitative phenotype measurements. From the curated quantitative data, the expected phenotype profile ranges were established through a meta-analysis pipeline using inbred rat strains in control conditions. The disease and qualitative phenotype annotations are propagated to their associated genes and alleles if applicable. Currently, RGD has curated nearly 1300 rat strains with disease/phenotype annotations and about 11% of them have known allele associations. All of the annotations (disease and phenotype) are integrated and displayed on the strain, gene and allele report pages. Finding disease and phenotype models at RGD can be done by searching for terms in the ontology browser, browsing the disease or phenotype ontology branches or entering keywords in the general search. Use cases are provided to show different targeted searches of rat strains at RGD.
Highlights
The laboratory rat (Rattus norvegicus) has been used as an animal model in biomedical research for over 150 years
The Strain Submission Form can be found via the ‘Submit Data’ link on the Rat Genome Database (RGD) homepage or on the menu bar of the Strain Search page, which can be accessed from the link in the center of the RGD homepage
Curated strains can be searched by genes, diseases or phenotypes, and the results can be imported into RGD tools or downloaded for customized analysis
Summary
The laboratory rat (Rattus norvegicus) has been used as an animal model in biomedical research for over 150 years. The genome-edited models confirm the causal effect of targeted genes and can be used as in vivo models to further study disease pathogenesis and treatment. These genome-modified rats, and selectively bred rats and their parental strains, have been used in a wide range of research in the fields of physiology, pharmacology, toxicology, nutrition, behavior, immunology and pathology. There are more than 1.6 million publications of rat research in PubMed, with about 35 000 being added every year. The Rat Genome Database (RGD; http://rgd.mcw.edu) was created in 1999 to organize the existing knowledge and present it to the research community with integrated genomic, genetic, phenotypic and disease datasets
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