Identification of candidate genes for the familial malignant melanoma tumor suppressor gene on 9p21

Recently the p16 gene has been localized to a region approximately 500 kb proximal to the IFN gene cluster on chromosome 9p21 that is frequently deleted in tumor cell lines. This gene has been put forth as a candidate for the familial melanoma locus. However as yet mutations in this gene have not been demonstrated in kindreds carrying the familial melanoma trait. We have identified a region of homozygous deletion in melanomas proximal to and independent of the region surrounding p16. We have constructed a YAC contig that extends 2-3 MB distal from D9S126 through D9S171 on chromosome 9p21. Utilizing markers generated from this contig, we have identified a distinct region of homozygous loss on 9p21 in melanoma tumors and cell lines. The deleted region spans approximately 300 to 600 kb, and is located >2 Mb proximal to the p16 gene on 9p21. It is entirely encompassed by two overlapping YACs. A cosmid contig comprising over 110 cosmids has been constructed from the YACs spanning the deletion, and these cosmids have been screened using exon trapping. Seventeen independent exon-trapped products have been identified from this novel region. STSs generated from the exons are currently being used to screen for deletionsmore » or mutations in melanoma cell line and tumor DNAs, as well as in melanoma kindreds demonstrating linkage of the trait to chromosome 9p21. The exons are expressed in various tissues, and cDNA clones containing them have been isolated and are presently being analyzed. The genes identified by this approach, by virtue of their deletion in melanoma samples independent of the more distally-localized p16 gene, are candidates for the familial malignant melanoma gene.« less