Doctor of Philosophy
Hill, Kathleen A.
Mus musculus is a human commensal species and an important model of human development and disease with a need for approaches to determine the contribution of copy number variants (CNVs) to genetic variation in laboratory and wild mice, and arising with normal mouse development and disease. Here, the Mouse Diversity Genotyping array (MDGA)-approach to CNV detection is developed to characterize CNV differences between laboratory and wild mice, between multiple normal tissues of the same mouse, and between primary mammary gland tumours and metastatic lung tissue.
A CNV detection pipeline was used in conjunction with evaluated probe sets, targeting 925,378 loci at an inter-probe-set median distance of 319 bp, to identify CNVs in a publicly-available dataset that includes representatives of 114 classical laboratory (CL) strain mice, 52 wild-derived (WD) mice, and 19 wild-caught (WC) mice. On average, WC and WD mice (~50 CNVs/mouse) have twice as many CNVs as CL mice. DdPCR confirmed 96% of MDGA-predicted copy number states. CL CNVs impact gene pathways related to immunity and nucleosome-associated functions, whereas olfaction and pheromone detection are impacted in WC mice. WD mice share impacted genic pathways with both cohorts.
In a five-member C57BL/6J inbred mouse family, losses of developmentally-important HOXA genes were detected and confirmed in multiple normal tissues. Further confirmation of postzygotic Hoxa13 losses in unrelated C57BL/6J, CBA/CaJ, and DBA/2J mice points to a widespread phenomenon occurring in mice, involving mutation hotspots and/or programmed losses.
In comparison to normal tissues (25 CNVs/mouse), cancer samples from an MMTV-PyMT mouse breast cancer model with lung metastasis have 1.6- to 3.2-fold more CNVs. CNV size is reduced and CNV recurrence is increased among primary tumours in the absence of the hyaluronan-mediated motility receptor, suggestive of altered mechanisms of CNV formation and selection for specific phenotypes in the tumour microenvironment, respectively.
CNVs were found to arise during normal development, producing different CNV profiles than with tumorigenesis and metastasis. CNV profiles also differ between laboratory and wild mice. This thesis presents improvements to an array-based CNV detection and analysis pipeline which was used to determine the contribution of CNVs to genetic variation in M. musculus.
Milojevic, Maja, "Characterization of genomic copy number variation in Mus musculus associated with the germline of inbred and wild mouse populations, normal development, and cancer" (2019). Electronic Thesis and Dissertation Repository. 6146.