JAX® Gene Mapping Service details
Crossing appropriate strains
To optimize marker density, the strain you cross to should be as unrelated as is practical to the mutant strain. We have pre-established marker panels for some of the more common strain combinations, such as C57BL/6J and 129S1/SvImJ, C57BL/6J and DBA/2J, and DBA/2J and BALB/cJ. We can develop new marker panels for other combinations.
Intercross or backcross?
If you have plenty of mouse room space, use an intercross. If the mutation is recessive and does not affect reproduction or birth, produce 80 F2 progeny out of which 20 or so should be affected (homozygous recessive). You will supply us with tail samples from those 20 offspring.
If you have a limited amount of mouse room space, use a backcross. Assuming the mutation is recessive and does not affect reproduction or birth, produce 40 N2 progeny (F1 backcrossed to affected parent), out of which 20 or so should be affected (homozygous recessive). You will supply us with tail samples from those 20 offspring. Ultimately, you will have to produce more 20 affected offspring to get the same mapping resolution that an intercross provides.
If you supply us with fewer samples than we request, the mapping resolution will be reduced.
Number of markers in the first and second scans
We use 80-100 SNP markers in the first (genome-wide) scan; we scan with four to eight additional markers to localize the mutation. To more finely localize the mutation, we scan with more markers from our SNP panel (up to the number in the region that are polymorphic between the two strains in the cross).
Tail samples or processed DNA?
We prefer that you send us tail samples. Send them on dry ice, individually labeled with your mice id numbers.
We will use DNA if you prepare it properly. Highly purified and correctly quantitated DNA is more likely to work. A two-mm tail snip should yield enough DNA for analysis. The Qiagen extraction kit or another comparable extraction method is preferred. The ideal DNA concentration is ~100-200ng/ul. DNA should be stored in 10mMTrisHCl or ddH20. (Tris EDTA (TE) should NOT BE USED as a storage buffer.)
Shipping the samples
Shipping all samples at the same time reduces your shipping and our processing costs.
Appropriate mapping projects
The method for mapping single gene traits will not work if the phenotype is being contributed to by multiple unlinked loci. Another reason for mapping failure would be if multiple similar or related phenotypes are segregating in the cross and being lumped together for mapping. Cases of severely reduced penetrance can also prevent discovery of the underlying gene location. If you need help in determining if any of these issues may be affecting your cross, please inquire before submitting a project.
Multi-integrated transgenes
Transgenes can integrate into multiple locations. Although we can identify a multi-integrated transgene, we cannot finely resolve its location. If our analysis indicates that the transgene has integrated into multiple locations, we will contact you immediately.
Fine mapping
Low resolution mapping may be adequate for determining if a mutation is a remutation at a previously known locus or at a novel site. However, to positionally clone or identify a mutation-causing sequence change, high resolution mapping is necessary, which means more DNA samples must be analzed (more affected offspring must be produced). Theoretically, 40 meioses (20 F2 or 40 N2 offspring) can give a maximum map resolution of 1/40 or 2.5 cM (roughly 5 MB). This may be sufficient to rule out previously identified genes and to identify flanking molecular markers that may be useful for more finely mapping a mutation. A large number of mice are not necessary for a single mapping run, as the most useful markers identified on a few mice can always be used again to type additional mice. However, enough breeding pairs must be set up to accomodate future mapping resolution needs.
