Identification of Melanoma Susceptibility Gene at 1p22

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DESCRIPTION (provided by applicant): Despite decades of research, metastatic cutaneous malignant melanoma (CMM) remains an incurable disease, demonstrating a median survival time of 9 months, with a 5-year survival rate of less than 5 percent. Further, over the past 20 years, the incidence of CMM has increased dramatically worldwide. Critical to this study, a positive family history of the disease is among the most established risk factors for CMM; 10% of CMM cases result from an inherited predisposition. Although mutations in two genes, CDKN2A and CDK4, confer an increased risk of CMM, they account for only 20% - 25% of families with multiple cases of CMM. We hypothesize that that there are additional CMM-predisposition genes, and this application provides an empirically based, technologically innovative approach to identify one such gene. We have performed a genome-wide linkage scan of 82 CMM kindreds with no involvement of CDKN2A or CDK4, and have identified a novel CMM susceptibility locus on chromosome 1 (1p22). To identify the melanoma susceptibility gene at this locus (Aim 1), we are integrating multiple experimental methods aimed at prioritizing candidate genes for mutation screening. Specifically, we will: (a) perform high-resolution SNP-typing and look for evidence of haplotype sharing between CMM families in order to further narrow the critical region; (b) design a custom oligonucleotide microarray representing all potential coding sequences within the 1p22 critical region in order to identify novel genes and to characterize tissue-specific gene expression for the purpose of candidate gene prioritization; and (c) design a custom 1p22 oligonucleotide microarray for comparative genomic hybridization (CGH) and look for partial- or whole-gene deletions in DNA from patient lymphocytes as well as melanoma cell lines with hemizygous loss at 1p22. Based on these data, we will prioritize our gene candidates and (d) screen genes for mutations using DNA sequencing. Following the identification of the 1p22 melanoma susceptibility gene, we will determine the prevalence of 1p22 gene mutation/loss (Aim 2) in a panel of melanoma cell lines, tumors, and nevi, and propose an experimental approach to understand its mechanism of action. Lastly, we will test the hypothesis that Iow-penetrance susceptibility alleles of the melanocortin receptor (MCIR) modify the penetrance of 1p22 susceptibility gene mutations (Aim 3) and genotype both affected and unaffected members of our 1p22-mutation positive families for these alleles.