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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Genome Scanning

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
  • Confirmation of C57BL/6 substrain background
Key benefits 
  • Cost-effective and reliable
  • Rapid turnaround
  • Available custom designed SNP panels specifically tailored for your needs

The right panel for your needs - $219.40/sample

Our genome scanning experts can assist you in identifying the right approach for your research application. We have a variety of standard and custom panels designed to meet your needs efficiently and reliably. Please inquire if what you need is not listed here as we have too many panels to list:

C57BL/6 substrain characterization panel distinguishes between C57BL/6J (B6J) and C57BL/6N (B6N) or C57BL/6NTac (B6NTac) genetic backgrounds.

C57BL/6 vs 129 panel distinguishes between C57BL/6 and 129S.  Please inquire about other 129 substrains.

Custom SNP panel of 150-200 informative polymorphic SNPs perfectly designed to meet your needs.

An additional $89 is charged for the two-way shipping of the sample kit.

Need additional information?
Contact us.

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

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 compare specific strain backgrounds or to facilitate marker-assisted breeder selection (for constructing congenic lines).

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. The Jackson Laboratory SNP panels are designed to have informative polymorphic SNP markers, evenly spaced, across the 19 autosomes and the X chromosome. SNP panels do not include any markers on the Y-chromosome. The number of SNP markers in each panel depends upon which 2-3 strains are being compared, however, the number of SNP markers ranges from 130-200.

What is the density of a genome scan?

We recommend using 150 SNP markers evenly spaced over the 19 autosomes and the X chromosome.

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 carrier females to wild-type recipient males to produce the F1 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.

How do I ship samples to test?

Upon your order, JAX® Services will provide a sample collection kit for you to ship your tissue samples to us for testing. The kit will include an instruction sheet, barcoded 96-well plate, optical-grade strip caps to seal the wells, a return form to provide samples IDs with the corresponding plate location, and a preaddressed/prepaid Fed Ex shipping envelope. Please do not send samples without the appropriate sample submission form. If you are sending DNA samples, your project manager will contact you with further instruction about sample submission when the project is initiated.

Do I need to ship the samples on ice?

No, we have validated the stability of the tissue sample collection kit under ambient shipping conditions. Do not freeze the samples or ship on ice. Ship the samples for next day delivery using the prepaid label in the sample collection kit. However, if you plan to send pre-extracted DNA, it must be shipped on dry ice. Please do not ship samples on a Friday or the day before a Federal US holiday.

Should I send you processed DNA or tail samples?

The sample collection kit has been validated with tail samples. We prefer to prepare DNA from your tail samples or ear notches. Please send us biopsies including appropriately sized tail tips or ear punch. We require approximately 1.5 mm – 2 mm of tail tip or ear notch per animal. Place one sample per well in the 96 well plate provided in the sample collect kit. If you are limited to only DNA samples, please contact JAX® Services to get sample submission guidelines and further instructions. We cannot guarantee results from DNA that is not extracted by the Jackson Laboratory.

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 or strains with >3 backgrounds present 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, 11-15 working days after we receive your samples.

One-time scanning projects

One-time scans are used to compare the presence of 2-3 known background strains. 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 11 to 15 work days after your samples arrive for your genome scan. At any time, you may contact your project manager by phone and email to request an update or to ask project related questions.

Can this genome scanning service be used to determine what genetic backgrounds are present if no background information is known or if I have contamination in my congenic line?

Generally not. Genome Scanning is only recommended if contamination is suspected from a specific, known source. If the source of contamination or starting background mix of a strain is unknown, a much higher density mouse genotyping arrays, such as GigaMUGA or MegaMUGA, should be utilized for analysis.

Can this genome scanning service detect genetic drift in my colony?

No. Genetic drift can occur in any place in the genome and may include single base changes, deletions, duplications, or inversions in the DNA. It’s unlikely that a SNP panel of any kind will happen to test the exact location or type of mutation that occurs spontaneously by genetic drift. Read this blog or check out our frequently asked questions to learn more about minimizing genetic drift.