LETTERS TO THE EDITOR Lack of Genetic and Epigenetic Changes in CDKN2A in

The strongest known epidemiologic risk factor for melanoma is a large number of melanocytic nevi (Swerdlow and Green, 1987), whereas the most important genetic risk factor is germline mutation of the CDKN2A gene, which encodes the cell cycle inhibitor p16 (Kamb et al, 1994; Nobori et al, 1994). CDKN2A mutations exist in some melanoma-prone families (reviewed in Hayward, 1996; Foulkes et al, 1997; Ruas and Peters, 1998), but account for only a small fraction of all familial melanoma (Platz et al, 1997; Aitken et al, 1999). Some melanoma kindreds include individuals with a high prevalence of ``dysplastic' ' (Greene et al, 1985) or ``atypical'' (Gruis et al, 1995) nevi, but this phenotype does not segregate with CDKN2A (reviewed in Hayward, 1996); however, evidence for linkage of ``common' ' nevus count with CDKN2A has been found in three melanoma pedigrees, only one of which carried an exonic mutation, suggesting that other variants in the region, outside the sequence encoding p16, affect nevus density (Cannon-Albright et al, 1994). We have shown by sib-pair linkage analysis that ±30 % of variance in moliness is due to genetic variation at or close to the marker D9S942 (Zhu et al, 1999), 15 kilobases upstream of CDKN2A, and we surmise that D9S942 is in disequilibrium with a functional polymorphism nearby. We hypothesize that as germline mutations in the exons of CDKN2A are rare, it is likely that variants in the noncoding regions of this gene are responsible for this major determinant of nevi, and by inference, of melanoma. Somatic changes and loss of heterozygosity (LOH) of CDKN2A support a role for this gene in nevus etiology (Healy et al, 1996a; Lee et al, 1997). Given the above links between CDKN2A, melanoma, and nevi, we looked for chromosomal loss, structural and epigenetic changes in the CDKN2A gene in benign melanocytic lesions. A 4 mm punch was used to separate neval from stromal tissue from 10 g paraf®n-embedded sections of 25 intradermal nevi and 25 compound nevi. Sections of nevi and stroma were incubated i