Genotyping Troubleshooting Guide

Genotyping mouse strains requires dedicated time and resources. Having a genotyping assay not working correctly can create headaches for you and possible delays in setting up new matings and your experiments. This page is designed to guide you to troubleshoot common problems with genotyping mice.


Consistent genotyping of mouse strains and effective troubleshooting of genotyping assays requires that you use appropriate controls every time you genotype your mice. The following table lists which controls you need to use.

Control (Mutant / Transgene)

Homozygous mutant/transgene

Heterozygote / Hemizygote**

Homozygous Wild Type / Noncarrier

No DNA Template (water)

When needed

When distinguishing between homozygotes and heterozygotes/hemizygotes*



Always (tests for contamination)

* If homozygotes are not produced in a mouse colony, then homozygous controls are not required. If homozygotes are embryonic lethal for example.

**If a colony is maintained as homozygous and no heterozygous/hemizygous controls are available, you can create a pseudo heterozygote/hemizygote control by mixing DNA for a homozygote and a wild type together in a 1:1 ratio.

If you are not using the appropriate controls, go back and re-genotype with the appropriate controls.

Four Common Genotyping Problems