Gene Mapping Service frequently asked questions

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What strains can I use for the mapping cross?

The Jackson Laboratory SNP markers have been tested against 103 commonly used inbred strains. Any of these strains can be used in a mapping cross. We recommend that the two strains used be as unrelated as is practical, to increase the potential marker density. We have pre-established marker panels for some of the more commonly used strain combinations, such as C57BL/6J and 129S1/SvImJ, C57BL/6J and DBA/2J, DBA/2J and BALB/cJ and many more. We can develop new marker panels for other strain combinations as needed.

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How do I determine whether an F2 or an N2 would be used for mapping in my project?

The differences in these two approaches are subtle. Both work well for mapping. If you have a recessive mutation that breeds well and have no major limitation in your mouse box space, you can breed F1xF1 and collect enough F2 animals to get 10 or more affected mice (about 40 offspring, best bred from several F1 intercross mating pairs to assure plenty of affected F2 homozygotes). If box space is limited, and you have a good supply of homozygous mutant parental animals, by producing an N2 (F1 backcrossed to affected parent) about one half instead of one quarter of the offspring will be affected homozygous mutant mice usable for the genome scan. Nevertheless, ultimately more offspring will need to be bred to get the same map resolution.

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How many markers do you look at for the first scan, how many markers for the second scan?

We may use 80-100 markers in the genome wide scan, and then select 4-8 additional markers to refine the position. If higher resolution is requested, we can add more markers in the candidate interval up to the number of markers from our set that are polymorphic with the particular strain combination in your cross.

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If I don't have the total number of samples you suggest (20 for a F2 and 40 for an N2), can you still map my gene?

Yes, though we may not be able to narrow the region as much as we could with the requested number of samples. Please contact us to discuss this situation.

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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. If you want to or have already prepared DNA from your mice, we can test your DNA preps in our system, and, if they work well, we can use them for the mapping. Highly purified and correctly quantitated DNA is more likely to work.

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If I extract my own DNA, what method and storage buffer should I use?

A 2 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).

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Why do you request the shipment of all samples for the project at one time?

Shipping all samples at the same time saves you shipping costs and it reduces our costs of processing your samples.

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What types of mapping projects would not be appropriate with this method?

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.

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Can you identify multi-integrated transgenes?

Please be aware that transgenes can integrate into multiple locations. While we do have the capability to identify a multi-integrated transgene, we will not be able to refine the location of the transgene. If our analysis indicates that the transgene has integrated into multiple locations, we will be sure to contact you immediately.

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When would you recommend additional breeding for a mapping project?

The answer depends on your goal. To simply check to see if the new mutation is likely to be a remutation at a previously known locus or at a novel site, lower resolution may satisfy this need. If you plan to positionally clone or identify the exact sequence change that has caused the mutation, more animals will be needed to generate a higher resolution map. 40 meioses (20 F2 or 40 N2) give a maximum theoretical map resolution of 1/40 or 2.5 cM (roughly equivalent to 5 MB genome wide average). This may be sufficient to rule out previously identified genes and to identify flanking molecular markers that may be useful in future refining of the map position. It is not necessary to have a large number of animals for a single mapping run, as the most useful markers identified on a few animals can always be run later on additional animals as they become available. It is important, however, to set up enough breeding pairs to anticipate future mapping resolution needs.

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