Physical and transcriptional characterization of a region on the short arm of chromosome 1 (1p21--p31): A novel locus implicated in hereditary malignant melanoma

The incidence of cutaneous malignant melanoma in Caucasian populations has been rising steadily leading to a significant increase in mortality and morbidity. In the United States, with the exception of lung cancer in women, its incidence has increased at a rate greater than any other neoplasm. Current estimates indicate that 5–10% of all melanoma cases have a genetic basis, 25% of which are due to mutations in the CDKN2A gene, indicating genetic heterogeneity. Therefore, our laboratory performed a genome-wide linkage study in 49 high-risk Australian families where the early onset age group showed significant linkage to the short arm of chromosome 1 (1p21–p31). This dissertation describes a detailed physical and transcriptional characterization of this novel melanoma susceptibility locus. A YAC based physical and transcript map has been constructed spanning the 25 Mb candidate region between markers D1S430 and D1S495 with one small gap. A series of YACs were identified and confirmed to map to this region by STS content mapping. When necessary, additional YACs were mapped to the contig by screening a commercially available YAC library and chromosome walking. Thirty known genes and 112 ESTs have been mapped against the YAC contig. Analysis of recombinants and haplotype data of individuals from linked families pointed to a 6 Mb region between markers ATA14B03 and D1S188 believed to be the melanoma 1p “critical interval”. Six ESTs from the region were chosen for further characterization, four of which have been cloned to full-length transcripts and their expression profiles have been determined. These genes were subjected to mutational analysis in affected individuals from linked families. In addition, eight biologically significant candidate genes within the interval were included in the mutational analysis. Although, a number of polymorphisms have been detected, no disease-associated mutation was found in these genes. The data presented in this study will eventually help to identify the gene for hereditary malignant melanoma. Once identified, it will help scientists to better understand the biology of melanoma and will aid in the development of more effective diagnostic and preventive strategies for melanoma as well as in identifying therapeutic targets.