Copy number variants (CNVs) are the most prevalent form of genetic

variation, in terms of mutation rate and the fraction of the genome that

they affect, thus having substantial impact on health and evolution.

Despite of that, it is unclear how CNVs and their mutation rates are

influenced by environmental factors. Studies that are based on

population genomic analyses are unable to detect de novo CNVs until

present at high frequency, so the environmental influence can only be

speculated for CNVs which are more or less fixed in a particular

population. Moreover, these analyses as well as analyses of families are

readily performed on genomes from somatic tissues, providing only

diploid copy number and leaving allelic copy numbers unknown. This

precludes accurate estimates of CNV frequency and mutation rates,

disease-associations and environmental influence. To overcome these

issues, the research proposed here will investigate the effect of

several environmental factors on CNV frequency in single sperm cells, by

using the most recently developed technology of simultaneous genome

sequencing of thousands of cells. Additionally, by performing high

throughput RNA sequencing, we will examine whether strong

transcriptional responses invoked by environmental factors during

spermatogenesis may promote CNVs at induced loci through replication

stress. The project will estimate the frequency of CNVs linked to

specific environmental exposures, many of which are suggested to

associate with genomic disorders, hence contributing to the

understanding of disease onset and pathogenesis. Given that the mouse

strain used in this study is one of the major mammalian genetic and

biomedical research models, the results are expected to be highly

relevant to humans. The proposed research represents an original

approach into the study of CNV mutation rate, with potential to provide

unprecedented power of de novo CNV detection and resolution of

environment-genome interactions.