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Colony management glossary



Mating of a mouse to a parent or, more usually, to one of the parental strains.


Genetic background refers to the make-up of the genome of the mouse, usually an inbred strain or combination of inbred strains. This is described as background as it is referring to the remaining genome, excluding the genetic alteration that is being studied. 

Block/blocking factor

A factor included in the experimental design to help account for a nuisance variable. For more information see Blocking a nuisance variable on the Experimental Design Assistant website.


An animal with at least one copy of the genetic alteration being studied.

Closed colony

A colony where no mice are introduced from outside the stock from generation to generation, and all matings are between animals from within the colony.


Strains that are identical to the inbred strain they were generated from, other than the genetic alteration that has been introduced.

Confidence interval

Can be taken as a range of plausible values for the mean. The precise definition of a 95% confidence interval of a mean is that 95% of the confidence intervals of this mean should, in the long run, contain the true mean. For an interactive visualisation of this concept see the R Psychologist website.


Strains that were made on one inbred strain but have been crossed for at least ten generations on to a different inbred strain. They will be almost genetically identical to the new inbred strain other than the GA. However, there is likely to be a small amount of residual chromosomal DNA from the original inbred strain.

Effect size

Quantitative measure of the difference between groups, or strength of relationships between variables.

Expansion cohort

A group of mice that are bred in order to increase the size of a colony. Offspring are intended for use as breeders rather than in experiments.


A factor (whether it is a factor of interest or a nuisance factor) is a mathematical construct (created when generating the experimental design) to allow the researcher to quantify an effect, also called a variable. This could be anything that can potentially influence the outcome of an experiment such as drug concentration, genotype, age or housing conditions. A factor of interest (also known as an independent variable of interest or a predictor variable) is a variable that the researcher manipulates (e.g. treatment, disease state, time) to answer a scientific question. For more information see Independent variable of interest on the Experimental Design Assistant website.

GA strain

Genetically altered strain. Genetically altered strains have induced mutations, including transgenes, targeted mutations (knockouts or knockins), retroviral-induced mutations, proviral-induced mutations or chemically-induced mutations.

Genetic drift

In the case of closed mouse colonies, genetic drift is the accumulation of random mutations in the genetic background, causing the colony to become different from the progenitor strain(s). For more information see Colony Management Best Practice: Refreshing the background strain to avoid genetic drift.

Inbreeding depression

A reduced biological fitness of the colony due to breeding related individuals together. Inbreeding depression is caused by detrimental alleles that have occurred through spontaneous mutations in every generation (genetic drift) becoming homozygous due to a closed breeding scheme (closed colony).


A cross between individuals heterozygous for alleles at a particular locus.


Mice that are on a mixed genetic background. Usually this is used to refer to mice that are being backcrossed but have not yet reached ten generations of backcrossing.

Nuisance variable

Variables that are not of primary interest but should be considered in the experimental design or the analysis because they may affect the outcome measure and add variability. For more information see Nuisance variable on the Experimental Design Assistant website.


A type of genetic cross in which an organism is crossed to a strain from which it was not recently derived.

Pilot study

A small experiment designed to test logistics and gather information prior to a larger study, in order to improve the latter’s quality and efficiency. Pilot studies can reveal deficiencies in the design of a proposed experiment or procedure, and these can then be addressed before animals, time and resources are expended on large scale studies. Sometimes pilot studies are used to assess adverse effects of drugs or procedures in a small number of mice before a larger cohort is used for the main study. For more information see the Conducting a pilot study resource.


For a predefined, biologically meaningful effect size, the probability that the statistical test will detect the effect if it exists (i.e. the null hypothesis is rejected correctly). The desired power for an experiment is one of the parameters used in a power calculation to estimate the sample size required for an experiment.


Allocation of animals to treatments so that each animal is equally likely to be assigned to receive each treatment. Randomisation also helps satisfy the statistical analysis assumption that results are independent. For more information see Randomisation on the Experimental Design Assistant website.

Recipient strain

Desired background strain that is mated with a GA strain to transfer a genetic mutation from the background it was generated on.

Sample size

Number of experimental units per treatment group. In in vivo experiments the experimental unit is often the animal (The experimental unit is the biological entity subjected to an intervention independently of all other units, such that it is possible to assign any two experimental units to different treatment groups.). Sample size should usually be calculated using a power analysis and should be the minimum required without undermining the scientific integrity of the experiment.

SNP/SNP panel

Single nucleotide polymorphism. A type of polymorphism in which two chromosomes differ in a given segment by the identity of a single base pair.  A SNP panel is a set of SNPs that can be used to confirm the identity of a strain using combinations of allele frequencies that are unique to each strain.


Holding stock - Cages of mice that are unmated and held, either for future experiments that are not yet defined or for breeding at a later date.

Future breeding stock - Young fertile males and females used to maintain the colony of mice.

Experimental stock - Males and females of a defined genotype or phenotype and age, with appropriate controls.

Intermediate stock - Mice that are generated as breeding stock in a complex breed. They will carry a subset of the final required genetic alterations or will not have all the alterations in the correct zygosity.


A colony of genetically similar mice with a defined genetic background (including inbred strains and progeny of specific genetic crosses), or a mixed population of mice with partially known genetic backgrounds, usually carrying specific genetic alteration(s).


Substrains occur when colonies are separated by more than 20 generations from the progenitor strain and are considered to be genetically distinct from the progenitor strain (see nomenclature guidelines at the Mouse Genome Informatics Database).


Increasing egg production up to ~30 eggs (compared to five to 15 eggs through natural ovulation) through use of hormones. Superovulation can be used with natural mating or IVF.

Tick-over/maintenance colonies

Colonies of mice that are bred in order to maintain stock as live colonies (rather than archiving). Tick-over/maintenance colonies are not usually used to provide mice for experiments but to ensure continuity of the strain for future experiments.


The effect of interest that the experiment is attempting to identify/quantify. For example, a treatment could be a pharmacological, phenotypic or husbandry intervention.

Trio mating

Mating combination of one male and two females in a cage.


Two experimental observations will rarely if ever be identical – the differences are due to random variability. Variability can be caused by biological effects, technical differences or analytical methods (for example).

Wild type

The phenotype with respect to a given inherited characteristic that is considered to be the "normal" type commonly found in natural populations.

Breeding and colony management