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

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.

快速同类系构建（Speed congenics）是构建同源导入小鼠以研究基因功能的关键工具，但当前用于该技术的单核苷酸多态性（SNP）基因分型方法成本高昂。我们依托高通量测序技术的优势，开发了一种高性价比、高密度的SNP基因分型检测方案，可适配多种回交品系组合。该检测方案覆盖1640个全基因组范围的SNP位点，这些位点在超过100个小鼠品系中均呈现多态性；每一对品系间平均可检测到549个诊断性SNP位点（标准差为136）。我们同时开发了一套用于SNP基因分型的生物信息学流程，可计算每个样本中与回交受体品系匹配的等位基因比例；该信息可用于指导下一代回交个体的筛选，并评估个体是否已成为同源导入小鼠。该检测方案还可应用于其他研究技术，包括数量性状位点（QTL）定位、标准F2杂交、祖源分析及法医鉴定。