A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power. Mus musculus

Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. We took advantage of the power of high throughput sequencing technologies to develop a cost-effective, high-density SNP genotyping assay that can be used across many combinations of backcross strains. The assay surveys 1,640 genome-wide SNPs known to be polymorphic across more than 100 mouse strains, with an expected average of 549 (standard deviation of 136) diagnostic SNPs between each pair of strains. We also developed a bioinformatic pipeline for SNP genotyping and calculating the percentage of alleles that match the backcross recipient strain for each sample; this information can be used to guide the selection of individuals for the next backcross, and to assess whether individuals have become congenic. The assay could also be used for other techniques including QTL mapping, standard F2 crosses, ancestry analysis, and forensics.