Genomic copy number variation in Mus musculus.

Authors

M Elizabeth O Locke, Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, CanadaFollow
Maja Milojevic, Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, CanadaFollow
Susan T Eitutis, Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, CanadaFollow
Nisha Patel, Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, CanadaFollow
Andrea E Wishart, Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, CanadaFollow
Mark Daley, Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, Canad & Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, CanadaFollow
Kathleen A. Hill, Department of Computer Science, The University of Western Ontario, London, ON, N6A 5B7, Canada & Department of Biology, The University of Western Ontario, Biological and Geological Sciences Building 1151 Richmond St. N, London, ON, N6A 5B7, CanadaFollow

Document Type

Article

Publication Date

7-4-2015

Journal

BMC genomics [electronic resource]

Volume

16

First Page

497

Last Page

497

URL with Digital Object Identifier

10.1186/s12864-015-1713-z

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.