Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species

Figure 3

Comparative genomics approach to mapping phenotypes. Functional genomics information within a model organism genome, such as the mouse genome, can provide relevant and high confidence information about genes in other mammalian genomes. Nine mouse genes associated with phenotype data obtained from knockout (KO) strains of mice are represented in the top left corner of Figure 3. The resulting bladder cancer related phenotypes are indicated by the colors of the individual genes and the corresponding colors on the lower left corner of Figure 3. The mouse genes are mapped to their one-to-one orthologs in the target genome of an endangered mammalian species. The resulting locations of the orthologous genes are annotated with the same phenotype as the mouse gene. Blue: increased urinary bladder carcinoma incidence; yellow: increased urinary bladder transitional carcinoma incidence; pink: abnormal urinary bladder urothelium morphology; and green: urinary bladder inflammation. Once the phenotypes are mapped to the target genome, SNPs most likely to disrupt the orthologs in the endangered species (nonsense mutations and frameshift mutations) provide potential genotype-phenotype associations that mirror the phenotypes observed in knockout mice.