Electronic Thesis and Dissertation Repository

Degree

Doctor of Philosophy

Program

Biology

Supervisor

Hill, Kathleen A.

Abstract

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.

Appendix 2A - Genome-Wide Human SNP Array 6.0 filtered probe list.txt (12400 kB)
Appendix 2B - Genome-Wide Human SNP Array 6.0 filtered probe list including flanking regions.txt (12116 kB)
Appendix 2C - 874 HapMap3 CEL files.csv (223 kB)
Appendix 2E - 351 Mouse Diversity Genotyping Array CEL files from The Center for Genome Dynamics at The Jackson Laboratory and sample ID.txt (10 kB)
Appendix 2F - List of Mouse Diversity Genotyping Array SNP probes from filtered probe list that produced a No Call genotype in all 351 mouse samples.txt (2 kB)
Appendix 2G - List of genes unlikely to vary in copy number.csv (52 kB)
Appendix 3A - Mouse sample information for 351 Mouse Diversity Genotyping Array CEL files.csv (22 kB)
Appendix 3B - Mouse sample cohort, subspecies and origin information for 215 Mouse Diversity Genotyping Array CEL files. .csv (27 kB)
Appendix 3C - Autosomal CNVs detected for 351 mouse samples.csv (1302 kB)
Appendix 3D - Chromosome X CNVs detected for 351 mouse samples.csv (140 kB)
Appendix 3E - Summary of autosomal and chromosome X CNVs detected for 351 mouse samples.csv (59 kB)
Appendix 3F - CNVs detected for 210 mouse samples.csv (607 kB)
Appendix 3G - Summary of autosomal and chromosome X CNVs detected for 210 mouse samples.csv (17 kB)
Appendix 3J - CNV and SNP genetic distance matrices.csv (1053 kB)
Appendix 3K - Ingenuity Pathway Analysis core analysis of genes overlapping CNV regions for different copy number states and two mouse cohorts.xls (53 kB)
Appendix 3M - List of CNVs found overlapping genes that are unlikely to vary in copy number.csv (6 kB)
Appendix 4A - Log R ratio, B allele frequency, and waviness factor values for 26 mouse tissue samples and two PennCNV runs.xlsx (15 kB)
Appendix 4B - CNV calls for first PennCNV dataset.xlsx (19 kB)
Appendix 4C - CNV calls for second PennCNV dataset.xlsx (17 kB)
Appendix 5A - CNV calls for six mammary gland primary tumour samples and six lung with metastasis samples from three MMTV-PyMT Rhamm-:- mice and three MMTV-PyMT Rhamm+:+ mice. .csv (37 kB)
Appendix 5B - CNV and SNP genetic distance matrices.csv (3 kB)
Appendix 5C - Copy number state, position and genic content of CNV regions that are recurrent in all three samples with a shared Rhamm genotype and tumour type.xlsx (13 kB)

Available for download on Saturday, April 18, 2020

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