The genotype of genetically modified mouse lines is monitored by researchers using small tissue or blood samples collected by skilled animal care staff. Samples are sent to the relevant research organization for analysis. Techniques use to monitor genotype include PCR (Polymerase Chain Reaction) a process that provides a DNA fingerprint, and flow cytometry, a process that analyses cell populations in blood samples. The genotype results are entered directly on to the animal facility database by researchers using a web interface. Once the genotype results are available researchers can select animals needed for research and animal care staff can select future breeders.

Most genetically modified mouse lines are maintained on an inbred strain background to minimise variability in research. Colonies of common inbred strains are maintained at Australian BioResources to facilitate backcrossing. Backcrossing of genetically modified mouse lines to a standard inbred strain at regular intervals minimises genetic drift. To ensure that the inbred strains bred at Australian BioResources are pure, mice are screened by independent laboratories using a known set of genetic markers.