The Application of Targeted and Exome Sequencing for the Identification of Spontaneous and Induced Mutations in Mice

The Jackson Laboratory has established a large collection of spontaneous and N-ethyl-N-nitrosourea (ENU) induced mouse mutants with a wide variety of medically relevant phenotypes. While spontaneous mutations can be quite complex, including single nucleotide polymorphisms (SNPs), transposon insertions, deletions, or inversions, ENU induced mutations are typically SNPs. The traditional method of identifying the causative mutation through genetic mapping and Sanger sequencing of candidate genes has been effective but is time consuming, requires large populations of mice and can be expensive. In addition, it is particularly challenging when the mutation is not in a coding sequence. With a size of over 3 GB, it is still too expensive to sequence the genomes of the many mutant strains of interest. The combination of array capture for targeted resequencing and/or exome capture followed by high-throughput sequencing on the Illumina GAIIX has greatly accelerated the pace at which mutations have be identified. In deciding what approach should be employed to identify a specific mutation, a number of factors must be considered; 1) Is the mutation spontaneous or ENU induced; 2) Have traditional mapping approaches been exploited, and if not, should they be; 3) If there is mapping data, what is the size of the genetic interval; 4) What data analysis tools will be required; This approach has led to the identification of many mutations that result in disease-relevant phenotypes including craniofacial disorders, neurodegeneration, neuromuscular dysfunctions, cholesterol biosysthesis and reproduction.