Nearly half of the genetic differences between individuals are rooted not in their nucleotide DNA sequences, but instead come from changes in chromosome structure known as copy number variations (CNVs). Such structural variation causes genes within certain genomic regions to deviate from the “normal” two copies found in a standard diploid cell. De novo gene copy number variations (CNV) are now recognized as a significant source for a wide range of human diseases, including autism spectrum disorder. However, the cellular mechanisms and environmental factors that contribute to copy number mutagenesis still are poorly understood. In the human germline, meiotic recurrent CNVs form through non-allelic homologous recombination (NAHR) between low copy repeat elements (LCRs). Such large repeated sequences are found at CNV hotspot regions of our genome, but are absent in Saccharomyces cerevisiae. To study LCR-mediated CNV pathways in this tractable model system, we modified a yeast chromosome through the introduction of engineered LCRs: 10 to 40 Kb segments of yeast DNA that we duplicated to simulate the NAHR substrates that exist in humans. The engineered LCRs flank allelic insertions of genes encoding resistance to geneticin and hygromycin (KanMX and HphMX, respectively) and the SFA1-CUP1 cassette that confers dose dependent resistance to copper and formaldehyde (CuFA). The segregation of these markers in the haploid cell progeny within tetrads is used to identity and classify CNV events. Normal allelic recombination produces cells that express one of each drug resistance marker (never both together), and intermediate resistance to CuFA. In contrast, interhomolog NAHR between the LCRs produces tetrads with a pair of haploid cells expressing (i) double drug resistance and hyper-resistance to CuFA, and (ii) double drug sensitivity and hypersensitivity to CuFA. These spores carry, respectively, recombinant chromosomes with reciprocal segmental duplication and deletion. Tetrads that contain an intersister NAHR event have a pair of spores with (iii) single drug resistance and hyper-resistance to CuFA, and another (iv) sensitive to both drugs and hypersensitive to CuFA. Finally, intrachromatid NAHR between the LCRs produces tetrads in which only one spore has a deletion of the markers, without an associated duplication. This system allows us to not only measure the overall frequency of de novo meiotic CNV, but also to determine the relative occurrence of each of the NAHR classes. We are using this approach to investigate meiotic CNV mechanisms and to interrogate the CNV stimulation activity of a diverse panel of candidate meiotic genes and environmental copy number mutagens. The experimental system will be described in the poster, with our initial analyses of the role of LCR size and distance from each other on the formation of CNVs.