The overarching aim of this thesis is to study the mechanisms by which giant congenital nevi form and to study if such mechanisms are targetable. Virtually nothing is known about genes conferring susceptibility to the development of giant congenital nevi, largely untreatable lesions which increase the risk of patients for development of neurocutaneous melanocytoma and malignant melanoma. To discover such genes, we utilized a nevusprone transgenic mouse model together with the Collaborative Cross (CC), a genetic resource for discovery of genes for complex diseases. It not only allows gene discovery, but also a systems genetics approach that enabled us to determine how the gene functions in vivo to modify the nevogenesis.We also show that the identity of somatic oncogenic mutation (e.g. in NRAS) does not always define the histopathological subtype of nevus, as is generally thought. In sum, we have performed an unbiased genetic screen and discovered a novel gene (Cdon), a dependence receptor of sonic hedgehog (Shh) as the modifier gene for nevus exacerbation. We then used three different mouse models to validate it as the causal gene and determine its mechanism of action. We also show that Shh pathway components are active in the epidermis adjacent to human congenital nevi (Chapter 2 and 3). In summary this is the first time a gene has been successfully mapped and functionally validated using CC. In Chapter 4 we discuss the result from an unbiased genetic screen to map the modifier gene for development of sub-cutaneous (hypodermis) metastasis using 45 CC strains. Gja1 which encodes a gap junction subunit connexion 43 (Cx43) is the best candidate. Our gene expression and protein expression studies suggest that Gja1 could be a strong candidate for further study of sub-cutaneous metastasis.In Chapter 5 we went on to study the gene expression of normal skin, melanocytoma and malignant melanoma samples from our NRAS-Cdk4 mouse model to study the transformation and progression of melanocytic lesions. Dusp6 a negative regulator of MAPK pathway was highly upregulated with transformation and progression. Our protein expression study validated this result on murine and human nevi versus malignant melanoma samples.3