Data from: The mouse universal genotyping array: from substrains to subspecies

Genotyping microarrays are an important resource for genetic mapping, population genetics and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations and for substrain-level identification of laboratory mice. In addition to 141,090 SNP probes, GigaMUGA contains 2,006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically-diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.基因分型微阵列是开展遗传作图、群体遗传学研究以及监测实验种群遗传完整性的重要技术资源。我们研发了小鼠通用基因分型芯片（Mouse Universal Genotyping Array, MUGA）系列的第三代产品——GigaMUGA，这是一款针对家鼠（Mus musculus）设计的、包含143259个探针的Illumina Infinium II型基因芯片。GigaMUGA的核心探针组针对协作杂交（Collaborative Cross）与多样性远交（Diversity Outbred）种群的遗传作图需求，以及实验小鼠的亚品系鉴定进行了优化。除了141090个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）探针外，GigaMUGA还包含2006个拷贝数检测探针，这些探针集中分布于小鼠基因组的结构多态性区域。我们通过500份高质量参考样本对该芯片的性能进行了表征，这些样本涵盖了实验近交品系、重组近交系、远交种群以及野生捕获小鼠。GigaMUGA在涵盖从实验小鼠亚品系到其他家鼠属（Mus）物种的多种遗传多样性样本中均表现出极高的信息含量。除了阐述该芯片的探针组成与性能表现外，我们还提供了详细的探针级注释信息以及质量控制建议。