Most seasoned mouse researchers know that a strain’s genetic background profoundly affects the phenotypes that their mutant and transgenic mice manifest. For example, both Lepob and Leprdb mutant mice develop fundamentally different diabetic phenotypes on the C57BL/6J and C57BLKS/J genetic backgrounds, as described in an earlier blog post. Knowing on which strain background your mutant mice are is critical not only for choosing the proper wild-type control strains for your experiments, but also for comparing data between mice that carry different mutations and for comparing data reported by other researchers for the same mutant strain.
But what do you do if you don’t know on which genetic background your mice are – for example, mice that you obtain from a colleague – or you want to confirm the contribution of a particular inbred strain to your mutant strain’s background – for example, in mice that you have been backcrossing to C57BL/6J to make a congenic strain? Fortunately, JAX offers a service that can assist with such identifications – Genome Scanning.
Genome Scanning is based on the analysis fully customizable panel of 150-200 informative polymorphic SNPs of single nucleotide polymorphisms (SNPs). Each marker is selectively chosen so it is polymorphic between two specific inbred strains. Therefore each marker is informative.
This tool is mainly used to determine the genetic background of a strain. If your strain is a known combination of only two strains – C57BL/6 and 129, for example – or, at most, three strains, then Genome Scanning is the best choice. Genome Scanning is also the preferred method for assessing genetic background via backcrossing, and is integrated fully with our Speed Congenic service.