Single Nucleotide Polymorphism (SNP) Genotyping Services

Genetic background characterization alerts you to genetic variation, which may eventually arise even in closed breeding programs, as well as via the introduction of contaminating genetic backgrounds through misbreeding. Charles River has microsatellite and SNP panels appropriate for the genetic monitoring of any inbred strain of mouse or rat, from detecting a genetic contamination to fine-mapping a transgene insertion point.

SNP Panels & Marker Assay

  • Mouse 384 SNP Complete Background Analysis Panel
  • Mouse 128 SNP C57BL/6 Substrain Panel
  • Mouse and Rat 32-Marker Assay for Contamination Detection


  • Verification of inbred and outbred backgrounds
  • Detection of genetic contamination
  • Assessment of genetic diversity in outbred animal models
  • Relatedness testing
  • Cell line characterization
  • Linkage analysis
  • Mutation mapping
  • Transgene insertion site mapping
  • Recombination event detection

Why is Background Strain Characterization Recommended?

Time and money may be wasted when experiments are performed with animals that are not of the expected background strain. Misbreedings can occur undetected, and errors may occur in pedigree records. Research models are often exchanged among many institutions, making their precise breeding history difficult to track. Additionally, congenic animals may not have been fully backcrossed, or information on the number of backcross generations may not be available. Given that these events may occur in even the best-managed colonies, animals (colony or experimental) should have their background strain confirmed.

Charles River recommends background strain characterization at the following times:

  • When establishing a closed breeding colony
  • When new strains are received from collaborators
  • During backcrossing (to check extent and/or for speed congenics)
  • If unusual phenotypes appear
  • At the commencement of a series of experiments
  • Annual monitoring of in-house colonies