| Title: | Genomic copy number variation in Mus musculus |
| Author(s): | Locke ME; Milojevic M; Eitutis ST; Patel N; Wishart AE; Daley M; Hill KA; |
| Address: | "Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, Canada. mlocke2@uwo.ca. 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. 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. 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. 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. 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. 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" |
| DOI: | 10.1186/s12864-015-1713-z |
| ISSN/ISBN: | 1471-2164 (Electronic) 1471-2164 (Linking) |
| 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). CONCLUSION: 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" |
| Keywords: | Animals DNA Copy Number Variations/*genetics Genetic Variation/genetics Genome/*genetics Genomics/methods Mice/*genetics; |
| Notes: | "MedlineLocke, M Elizabeth O Milojevic, Maja Eitutis, Susan T Patel, Nisha Wishart, Andrea E Daley, Mark Hill, Kathleen A eng Research Support, Non-U.S. Gov't England 2015/07/05 BMC Genomics. 2015 Jul 4; 16(1):497. doi: 10.1186/s12864-015-1713-z" |
