Genome Scanning Service

JAX-designed SNP panels are used to develop congenic lines in your lab, confirm strain identity, and monitor genetic quality.

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We have a unique selection of mouse single nucleotide polymorphism (SNPs) panels useful for a diverse set of mouse research applications.

Applications of SNP scanning services

  • Development of congenic mouse lines. 
  • Identification of strain background contamination. 
  • Confirmation of strain backgrounds.
  • Confirmation of C57BL/6 substrain background.
Key benefits 
  • Cost-effective and reliable.
  • Rapid turnaround.
  • Available custom designed SNP panels specifically tailored for your needs.

Select from our two panels 

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

C57BL/6 substrain characterization panel — $159/sample

Our B6 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.

Custom SNP Panel — $159/sample
Fully customizable, our panels 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

Need additional information?
Contact us.

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

Frequently Asked Questions

What is genome scanning analysis?

The Jackson Laboratory offers single nucleotide polymorphism (SNP)-based genome scanning services for researchers who breed animals in their home facility. This involves using a panel of SNP markers to distinguish between two or three strains of mice.

Our genome scanning service can be used to evaluate certain strain mixtures, to facilitate marker-assisted breeder selection (for constructing congenic lines), to map new mutations, or to detect/measure recent strain contamination. A similar service can be used to map new mutations.

Investigators provide tissue or DNA samples from the animals of interest. The Jackson Laboratory conducts SNP analysis and summarizes the percentage of desired genetic background in each sample submitted and recommends breeders for the next generation.

What is the density of a genome scan?

For the first generation scanned in a project, we recommend using 150 SNP markers evenly spaced over the 19 autosomes. This gives a density of 15 Mbases. We can scan the X chromosome if requested.

What is genome scanning used for?

This service is tailored to scan multi-generations, supporting the development of speed congenic strains, but it can also be used for a one-time scan to characterize a strain or to detect recent contamination.

How many animals should be scanned to develop a speed congenic?

Scanning 15-19 samples at each generation gives the best odds of finding two animals with high enough percentages of recipient genome to produce fully congenic mice in five generations of backcrossing. Six animals is the minimum number of samples we recommend scanning per generation to produce a congenic line. When scanning less than 15-20 animals, it may take more than 5 generations to get a fully congenic line. With certain strains, it may be easier and quicker to scan fewer animals (8-10) per generation (to N6 or N7) than to produce 19 samples per generation. If you send 15-19 samples for some generations and 7-10 for others, 5-6 generations may be necessary to produce a fully congenic line. If 4-6 animals are scanned per generation, 7-9 generations may be necessary to produce fully congenic animals.

What is the best breeding scheme for producing 19 animals per generation?

To produce the largest number of animals at each generation, select two male animals per generation and rotate them through 3 sets of 2 females, leaving the male with the females for one week. This scheme generates up to 12 litters in three weeks.

Do I send samples from all animals produced from each generation?

Because you will be mating only the animals that carry the gene of interest, it is cost efficient to scan only the animals carrying the gene of interest. You should genotype the animals and send only the heterozygous animals for genome scanning. We suggest fixing the sex chromosome through breeding (see recommendations below).

Do I send F1 animals to be scanned?

No, we do not scan the F1 animals. All F1 animals have one allele from each parent at every locus. F1 animals will scan as 50% from each parental strain.

How do I fix the sex chromosome through breeding?

The best way to fix the Y chromosome is to backcross 6 F1 carrier females to wild-type recipient males to produce the N2 generation. To fix the X chromosome, mate wild-type recipient females to carrier males for the remaining generations. At generations N2-N5, scan male carriers and backcross the best two. At each generation, we recommend selecting 2 males and rotating them though 3 sets of 2 wild-type females, leaving the male with the females for a week. This optimizes chances of producing enough similar-aged offspring to test for the next generation. Note: Mating the F1 female and the N2 and N3 males fixes both sex chromosomes. If requested, X chromosome markers can be included in the scan.

Should I send you processed DNA or tail samples?

We prefer to prepare DNA from your tail samples. Please send tissues on dry ice, individually labeled with your animal id numbers.

We can use DNA you have prepared, but our success rate is higher with DNA that we extract. More highly purified and correctly quantitated DNA is more likely to work. The ideal concentration is approximately 100-200 ng/µl. The DNA should be stored frozen in 10 mM TrisHCL or ddH2O. Note: EDTA inhibits the SNP reaction and should not be present in a concentration greater than 0.1 mM.

Do I need to know the background of my strain?

Yes. Because we select polymorphic markers for each project, it is necessary to know the background of your strain. Undefined strains such as outbred strains are not recommended for genome scanning.

Can you scan an outbred strain?

Because we use a panel of SNP markers that are polymorphic between the strains of origin, and an outbred strain by nature has multiple possible alleles at any given locus, we prefer not to scan strains that are derived from outbred strains. If your strain is derived from an outbred strain, contact JAX® Services to discuss the viability of the project.

How long will it take to get the results of a genome scan?

Depending on the complexity of your project, 10-12 working days after we receive your samples.

How do I find out about the status of my project?

By contacting your assigned project manager or JAX® Services by phone and email.

One-time scanning projects

One-time scans can be used to evaluate certain strain mixtures or to detect/measure recent strain contamination. For all one-time scan projects, other than projects to confirm that a strain is fully congenic, please contact us to discuss the viability of the project.

How do I find out about the status of my project?

At the beginning of your project, your assigned project manager will contact you and provide their contact information. You will be sent the results of your genome scan within 10 to 12 days after your samples arrive for your genome scan. At any time, you may contact your project manager to request an update or to ask project related questions.