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Mouse genotyping library

The mouse (Mus musculus) is a classic vertebrate model organism and is widely used for genetic research. As the mouse has extensive similarity to humans in terms of anatomy, physiology and genetics, research in mice can be applied to investigations into human disease. The availability of inbred lines, and the natural variation between them, facilitates research into complex diseases that involve the interaction of multiple genes.  

The mouse library, developed in conjunction with The Jackson Laboratory, Maine, USA offers a set of 1,638 pre-validated assays for mouse genotyping. These single nucleotide polymorphism (SNP) markers were selected from publically available databases and the KASP assays were validated across DNA from the majority of popular laboratory mouse strains. The library provides a powerful tool for the mapping of traits within mouse disease models and breeding populations. The Excel file contains the list of available mouse assays, and also details the genetic variation between the popular strains of laboratory mice at these SNP locations.  

The development of the mouse library is detailed in full in the following scientific publication:
Development of a SNP Genotyping Panel for Genetic Monitoring of the Laboratory Mouse. Genomics 83 (2004) 902-911).

Use of KASP to develop speed congenics

Congenic strains of mice typically require 10 generations of backcrossing to generate, which can be a time-consuming process. The time involved in creating congenic mice can be significantly reduced through the use of marker-assisted selection (MAS), and this is termed ‘speed congenics’. Genetic markers, such as SNPs, are used to identify mice from the second generation of backcrossing that contain the highest percentages of the desired genome; these mice are then used as parents for the subsequent generation. This MAS procedure is repeated for each subsequent generation, and hence enables congenic mice to be attained after only three or four generations of backcrossing. The mouse library offers a set of pre-validated KASP genotyping assays that can be easily applied to the development of speed congenics.  


  • Panel includes over 1,600 functionally validated SNP assays
  • Pick and choose the assays that are relevant to your research
  • No minimum order – order from 1 to 1600+ assays from the library 

  • KASP assays are easy to run in your own laboratory or can be used in a genotyping service project
  • No labelling of target-specific primers is required 

  • Only minimal DNA material required.


The mouse library assays can be provided as part of our genotyping service or as reagents to run KASP genotyping in your own laboratory. To place an order for pre-validated mouse library assays, download the Excel file containing the list of available mouse assays. Identify the assays that you require and paste the KASP assay IDs (from column A in the Excel file e.g. 01-004147733-M, 03-044237869-M) into the SNP submission template. Mouse panel assays for running in your own laboratory will be charged as custom SNP assays without validation as they have been pre-validated for inclusion in the panel. For enquiries about a genotyping service project please request a quotation or contact our customer services team.

To place an order, download the Marker excel file and copy and paste the required IDs into the Excel ordering template.

Make an enquiry Genotyping

Related downloads

Mouse marker 3.6MB


Jackson laboratory 769KB

genetic quality report

Jackson Laboratory – mammalian genetics research to enhance human health 929KB

Application note: Trans-regulation of mouse meiotic recombination hotspots by Rcr1.

Jackson Laboratory – mammalian genetics research to enhance human health 166KB

Case study: implementation of KASP genotyping in mouse genomics studies at the Jackson Laboratory

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Fact sheet