JAX® Genome Scanning Service

We have a unique selection of mouse single nucleotide polymorphism (SNPs) panels useful for a diverse set of mouse research applications including the development of new congenic mouse lines and identification of strain background contamination. Economical and reliable, we offer pre-validated 1500 SNP panel for mouse projects requiring the most rapid turnaround, Custom SNP panel specifically tailored for your experiments and a C57BL/6 substrain characterization panel to confirm your B6 strain.

SNP scanning applications for our three panels

  • Developing congenic mouse lines
  • Confirming strain backgrounds
  • Revealing strain background contamination
  • Confirming B6 substrain background


Select from our three panels

Our genome scanning experts can assist you in identifying the right approach for your research application.

Pre-validated 1500 SNP Panel — $235/sample

A pre-validated set of 1500 SNPs, including single nucleotide polymorphisms from panels previously offered at JAX.

  • Highly cost-effective and rapid turnaround
  • SNP density of 1-2 MB
  • Bonus! Includes a 150 SNP panel that distinguishes between C57BL/6J and C57BL/6N substrain backgrounds

Genome Scanning Services Project Quote form


Custom SNP Panel — $159/sample

Fully customizable, our panel of 150-200 informative polymorphic SNPs are perfectly designed to meet your needs.

  • Ultimate flexibility, only use SNPs that optimally support your project
  • SNP density of 15-20MB evenly spaced throughout the genome
  • Customized marker density of a specific genomic region

Genome Scanning Services Project Quote form


C57BL/6 Substrain Characterization Panel — $159/sample

C57BL/6J is the progenitor strain from which all other B6 substrains have been derived. Our newly developed panel can prevent costly misinterpretation of research results that arise from genotypic and phenotypic B6 substrain differences.

  • Cost-effective and rapid
  • Distinguishes between C57BL/6J (B6J) and C57BL/6N (B6N) genetic backgrounds
  • Uses 150 validated SNP markers spaced evenly throughout the genome, covering all autosomes and the X chromosome

Genome Scanning Services Project Quote form

Frequently Asked Questions

View our FAQ's regarding our genome scanning services, including sample collection, project expectations, and guidance on when to use each panel.

Other Services

Need additional information?
Contact Us.

  • Email jaxservices@jax.org
  • Toll free: 1-800-422-6423 (US, Canada & Puerto Rico)
    or 1-207-288-5845 (from any location)