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).

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.

Fig. 1

CNV call summary. Sankey diagram depicting CNV calls on the autosomes classified into unique categories stacked vertically for length, type, mouse strain type, uniqueness and gene content from left to right. Flows between vertical categories (in grey) are proportional to the number of calls sharing both horizontally neighboring classifications. For example, almost half of the “100 + kb” classified CNV calls are also “Amplifications”

Fig. 2

Number and recurrence of CNV calls. Each CNV call is represented as a single dot within larger circular clusters, with each cluster representing the autosomes 1–5, then 6–10 and so on. Calls with at least 40 % reciprocal overlap are joined by a line and considered recurrent. Each dot is then coloured on a heatmap scale, based on how many overlaps that call has with other calls on the same chromosome. The heat map colours range from 0 overlaps (dark blue) to 175 overlaps (red, chosen as it is half the number of total samples present). The total size of each chromosomal cluster is proportionate to the number of events found on that chromosome. Larger collections of connected dots represent CNV calls that are found in many samples, while unconnected dots represent unique events not shared among any samples. Labels A through D indicate complex clusters

Fig. 3

Copy number variants identified. For each chromosome both unique calls and recurrent regions are plotted. The unique calls are plotted for each chromosome as follows (listed from top to bottom): copy number amplification calls for three or more copies are plotted in dark blue above the region of the chromosome where they are found, the chromosome line in black, followed by one copy deletions in light red and full deletions in dark red below the chromosome line. The regions of recurrent CNV calls are plotted directly on the black chromosome line. Here, if the overlapping calls were all deletions, they are plotted in red; If they were all amplifications they are plotted in blue; If they are a mix of amplifications and deletions they are plotted in green

Fig. 4

SNP and CNV distance for MGI priority and 17 genomes project strains. a. Neighbor joining tree constructed using SNP distance. b. Multidimensional scaling (MDS) for SNP distance matrix, showing first two principle coordinates. c. Neighbour joining tree constructed using CNV distance. Trees are not proportional to each other. The dashed line for MA/MyJ indicates a manually shortened branch. d. MDS for CNV distance matrix. All diagrams are coloured based on similarity in SNP distance (panel a)