title: Genomic copy number variation in Mus musculus.
abstract: BACKGROUND
  Copy number variation is an important dimension of genetic diversity and has implications in development and disease. As an important model organism, the mouse is a prime candidate for copy number variant (CNV) characterization, but this has yet to be completed for a large sample size. Here we report CNV analysis of publicly available, high-density microarray data files for 351 mouse tail samples, including 290 mice that had not been characterized for CNVs previously.
  
  
  RESULTS
  We found 9634 putative autosomal CNVs across the samples affecting 6.87% of the mouse reference genome. We find significant differences in the degree of CNV uniqueness (single sample occurrence) and the nature of CNV-gene overlap between wild-caught mice and classical laboratory strains. CNV-gene overlap was associated with lipid metabolism, pheromone response and olfaction compared to immunity, carbohydrate metabolism and amino-acid metabolism for wild-caught mice and classical laboratory strains, respectively. Using two subspecies of wild-caught Mus musculus, we identified putative CNVs unique to those subspecies and show this diversity is better captured by wild-derived laboratory strains than by the classical laboratory strains. A total of 9 genic copy number variable regions (CNVRs) were selected for experimental confirmation by droplet digital PCR (ddPCR).
  
  
  CONCLUSIONS
  The analysis we present is a comprehensive, genome-wide analysis of CNVs in Mus musculus, which increases the number of known variants in the species and will accelerate the identification of novel variants in future studies.
authors.affiliation: Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, Canada. mlocke2@uwo.ca.
authors.forename: M Elizabeth O
authors.initials: ME
authors.lastname: Locke
authors.affiliation: Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada. mmiloje2@uwo.ca.
authors.forename: Maja
authors.initials: M
authors.lastname: Milojevic
authors.affiliation: Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada. seitutis@uwo.ca.
authors.forename: Susan T
authors.initials: ST
authors.lastname: Eitutis
authors.affiliation: Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada. npatel68@uwo.ca.
authors.forename: Nisha
authors.initials: N
authors.lastname: Patel
authors.affiliation: Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada. awishar@alumni.uwo.ca.
authors.forename: Andrea E
authors.initials: AE
authors.lastname: Wishart
authors.affiliation: Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, Canada. mark@daleylab.org.|Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada. mark@daleylab.org.
authors.forename: Mark
authors.initials: M
authors.lastname: Daley
authors.affiliation: Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, Canada. khill22@uwo.ca.|Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, Canada. khill22@uwo.ca.
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: Hill
mesh_terms: D000818:Animals; D056915:DNA Copy Number Variations / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods; D051379:Mice / Q000235:genetics*