The Systems Genetics Core Facility at UNC provides Collaborative Cross mice; genotyping services using the MUGA arrays and tools to utilize both the mice and the genotypes.
The Collaborative Cross is a genetic reference population derived from eight inbred strains by an international consortium of researchers. The Systems Genetics Core Facility (SGCF; http://csbio.unc.edu/CCstatus/index.py?run=AvailableLines) at UNC distributes CC lines that have reached a defined minimum level of inbreeding. The SGCF has also reconstructed the founder mosaic of each CC line. We have combined these reconstructions with the whole genome sequence published by the Sanger Institute to generate pseudogenomes from each CC line that incorporate all high quality SNP and indel variants while retaining the extensive annotation of the mouse reference genome (http://csbio.unc.edu/CCstatus/index.py?run=Pseudo). We are currently sequencing mice from each of the distributable lines and expect to make those genomes available before the end of 2016.
The SGCF has distributed CC mice to >40 laboratories. CC projects fall into four categories: Strain surveys to determine the genetics of a wide variety of traits; Follow up experiments in smaller sets of CC strains; Development of models of human disease and Identification and genetic and molecular dissection of novel biological phenomena. Manuscripts using the CC have been published recently including a strain survey for susceptibility of Ebola virus infection, a new mouse model for spontaneous colitis, the discovery of a meiotic drive system and a new parent of origin effect on gene expression. We will present summaries on the status of the CC population (number of lines, inbreeding and breeding performance); use of the CC and publications.
Genotyping arrays using iterations of the Mouse Universal Genotyping Array (MUGA) have been designed at UNC and implemented through GeneSeek (Neogen) in Nebraska. MUGA (7000 SNPs), MegaMUGA (70,000 SNPs) and GigaMUGA (150,000 SNPs) have each required separate and improved tools which are all available at http://csbio.unc.edu/CCstatus/index.py?run. The reissuance of the MUGA array can also be very useful for F2 analysis.